| Yerisiam | ire | 1813 | Proto-Southwest Cenderawasih Bay |
| Yawa Wadapi-Darat | yva | 44 | Proto-North Yawa-Saweru |
| Yawa Turu | yva | 61 | Proto-South Yawa-Saweru |
| Yawa Tarau | yva | 194 | Proto-South Yawa-Saweru |
| Yawa Rosbori | yva | 342 | Proto-North Yawa-Saweru |
| Yawa Mariadei | yva | 10 | Proto-South Yawa-Saweru |
| Yawa Mantembu | yva | 58 | Proto-North Yawa-Saweru |
| Yawa Konti Unai | yva | 37 | Proto-North Yawa-Saweru |
| Yawa Kampung Baru | yva | 13 | Proto-North Yawa-Saweru |
| Yawa Central | yva | 11 | Proto-North Yawa-Saweru |
| Yawa Ariepi | yva | 71 | Proto-North Yawa-Saweru |
| Yawa Ambaidiru | yva | 50 | Proto-North Yawa-Saweru |
| Yaur | jau | 1351 | Proto-Southwest Cenderawasih Bay |
| Yahadian | ner | 989 | Proto-South Bird's Head |
| Wooi | wbw | 53 | Proto-West Yapen Nuclear |
| Wetan | | 34 | Proto-Kisar-Luangic |
| West Tarangan | txn | 77 | Proto-Aru |
| West Makian Talapao | mqs | 547 | Proto-West Makian |
| West Makian Tagono | mqs | 110 | Proto-West Makian |
| West Makian Tafasoho | mqs | 110 | Proto-West Makian |
| West Makian Sabale | mqs | 228 | Proto-West Makian |
| West Makian Ngofabobawa | mqs | 110 | Proto-West Makian |
| West Makian Malapa | mqs | 111 | Proto-West Makian |
| West Makian Bobawa | mqs | 112 | Proto-West Makian |
| West Makian | mqs | 465 | Proto-West Makian |
| Watubela | wah | 49 | Proto-Seram Laut |
| Waropen | wrp | 11 | Proto-SHWNG |
| Warembori | wsa | 406 | Proto-SHWNG |
| Wamesa Wandamen | wad | 12 | Proto-West Yapen |
| Wamar | | 77 | Proto-Aru |
| Waioli | wli | 234 | Proto-Sahu |
| Wabo | wbb | 465 | Proto-East Yapen |
| Uruangnirin Tubiruasa | urn | 50 | Proto-North Bomberai |
| Uruangnirin | urn | 115 | Proto-North Bomberai |
| Umar | gop | 947 | Proto-Southwest Cenderawasih Bay |
| Ujir | udj | 292 | Proto-Aru |
| Tobelo | tlb | 230 | Proto-Tobelo |
| Tobati | tti | 23 | Proto-Oceanic |
| Tidore | tvo | 2119 | Proto-Ternate-Tidore |
| Ternate | tft | 229 | Proto-Ternate-Tidore |
| Teor | tev | 49 | Proto-Teor-Kur |
| Tehit Wersar | kps | 122 | Proto-Tehit |
| Tehit Teminabuan | kps | 661 | Proto-Tehit |
| Tehit Tehijit | kps | 160 | Proto-Tehit |
| Tehit Sodorfoyo | kps | 40 | Proto-Tehit |
| Tehit Sisir | kps | 41 | Proto-Tehit |
| Tehit Sidi | kps | 50 | Proto-Tehit |
| Tehit Seribau | kps | 292 | Proto-Tehit |
| Tehit Sawiat | kps | 169 | Proto-Tehit |
| Tehit Sasnek | kps | 83 | Proto-Tehit |
| Tehit Salmit | kps | 192 | Proto-Tehit |
| Tehit Sadrofo | kps | 43 | Proto-Tehit |
| Tehit Konda | kps | 82 | Proto-Tehit |
| Tehit Eles | kps | 78 | Proto-Tehit |
| Tehit | kps | 127 | Proto-Tehit |
| Tandia | tni | 129 | Proto-SHWNG |
| Taliabu | tlv | 1444 | Proto-Saluan-Banggai |
| Tabaru | tby | 227 | Proto-Tabaru |
| Sumuri Tomage | tcm | 48 | isolate |
| Sumuri Inorah | tcm | 57 | isolate |
| Sumuri | tcm | 158 | isolate |
| Suboo | | 791 | Proto-Central Alor |
| Sougb | mnx | 589 | Proto-East Bird's Head |
| Serui-Laut | seu | 11 | Proto-West Yapen Insular |
| Serewen | pmo | 38 | Proto-West Yapen Nuclear |
| Semimi | etz | 209 | Proto-Mairasi |
| Sekar Kokas | skz | 410 | Proto-North Bomberai |
| Seget Salawati | sbg | 154 | Proto-Segetic |
| Seget | sbg | 494 | Proto-Segetic |
| Saweru | swr | 424 | Proto-South Yawa-Saweru |
| Sawai Weda | szw | 1097 | Proto-Central-Eastern South Halmahera |
| Sawai Foya-Mafa | szw | 122 | Proto-Central-Eastern South Halmahera |
| Sawai | szw | 1084 | Proto-Central-Eastern South Halmahera |
| Saparua Malay | | 11 | Proto-Malay |
| Salkma Sayosa | msg | 372 | Proto-Klabra-Salkma |
| Salkma | msg | 458 | Proto-Klabra-Salkma |
| Sahu | saj | 225 | Proto-Sahu |
| Roon | rnn | 355 | Proto-Nuclear Biakic |
| Puragi | pru | 767 | Proto-South Bird's Head |
| Proto-Western Malayo-Polynesian | | 7369 | Proto-Malayo-Polynesian |
| Proto-Southern South Halmahera | | 28 | Proto-South Halmahera |
| Proto-SHWNG | | 25 | Proto-Eastern Malayo-Polynesian |
| Proto-Philippine | | 1973 | Proto-Malayo-Polynesian |
| Proto-Oceanic | | 2637 | Proto-Eastern Malayo-Polynesian |
| Proto-Mongondow | | 842 | Proto-Gorontalo-Mongondow |
| Proto-Malayo-Polynesian | | 2789 | Proto-Austronesian |
| Proto-Gorontalo-Mongondow | | 874 | Proto-Malayo-Polynesian |
| Proto-Gorontalo | | 857 | Proto-Buol-Gorontalo |
| Proto-Eastern Malayo-Polynesian | | 67 | Proto-Central-Eastern Malayo-Polynesian |
| Proto-Central-Eastern Malayo-Polynesian | | 180 | Proto-Malayo-Polynesian |
| Proto-Buol-Gorontalo | | 703 | Proto-Gorontalo-Mongondow |
| Proto-Austronesian | | 1771 | |
| Pom | pmo | 383 | Proto-West Yapen Nuclear |
| Patani | ptn | 952 | Proto-Central-Eastern South Halmahera |
| Papuma | ppm | 62 | Proto-West Yapen Nuclear |
| Papuan Malay | pmy | 518 | Proto-Malay |
| Pamona Ampana | pmf | 54 | Proto-Malayo-Polynesian |
| Pagu | pgu | 949 | Proto-Pagu |
| Onin Tawar | oni | 52 | Proto-North Bomberai |
| Onin Rumbati | oni | 53 | Proto-North Bomberai |
| Onin | oni | 455 | Proto-North Bomberai |
| Oirata | oia | 806 | Proto-FRATA |
| North Moluccan Malay | max | 711 | Proto-Malay |
| North Moluccan Javanese | jav | 593 | Proto-Malayo-Polynesian |
| Munggui | mth | 116 | Proto-West Yapen Nuclear |
| Mpur Saukorem | akc | 89 | Proto-Mpur |
| Mpur Mumbrani | akc | 40 | Proto-Mpur |
| Mpur Kebar | akc | 123 | Proto-Mpur |
| Mpur Anjai | akc | 40 | Proto-Mpur |
| Mpur Amberbaken | akc | 14 | Proto-Mpur |
| Mpur | akc | 1302 | Proto-Mpur |
| Moskona Merdey | mtj | 40 | Proto-East Bird's Head |
| Mor | moq | 202 | isolate |
| Moor | mhz | 1701 | Proto-SHWNG |
| Moluccan Javanese | jav | 20 | Proto-Malayo-Polynesian |
| Moi Waliam | mxn | 238 | Proto-Moi |
| Moi Waipu | mxn | 235 | Proto-Moi |
| Moi Suatolo | mxn | 55 | Proto-Moi |
| Moi Makbon | mxn | 588 | Proto-Moi |
| Moi | mxn | 637 | Proto-Moi |
| Modole | mqo | 966 | Proto-Modole |
| Miyah Senopi | | 40 | Proto-North Maybrat-Miyah |
| Miyah Pef Tintum | | 51 | Proto-North Maybrat-Miyah |
| Miyah Feif | | 47 | Proto-North Maybrat-Miyah |
| Miyah | | 525 | Proto-North Maybrat-Miyah |
| Meyah Mumbrani | mej | 42 | Proto-East Bird's Head |
| Meyah Akrin | mej | 40 | Proto-East Bird's Head |
| Meyah | mej | 1680 | Proto-East Bird's Head |
| Mer | mnu | 208 | Proto-Mairasi |
| Meher | kje | 2743 | Proto-Kisar-Luangic |
| Mbaham Patimuni | bdw | 120 | Proto-Mbaham-Iha |
| Mbaham Mambunibuni | bdw | 47 | Proto-Mbaham-Iha |
| Mbaham Horabena | bdw | 52 | Proto-Mbaham-Iha |
| Mbaham | bdw | 1913 | Proto-Mbaham-Iha |
| Maˈya Misool | slz | 454 | Proto-Maya-Matbat |
| Maˈya Kaplol | slz | 441 | Proto-Maya-Matbat |
| Maˈya | slz | 106 | Proto-Maya-Matbat |
| Maybrat Yaksora | ayz | 51 | Proto-Maybrat-Miyah |
| Maybrat Western | ayz | 18 | Proto-Maybrat-Miyah |
| Maybrat West Ayfat | ayz | 167 | Proto-Maybrat-Miyah |
| Maybrat Tehak Besar | ayz | 244 | Proto-Maybrat-Miyah |
| Maybrat Susumuk | ayz | 97 | Proto-Maybrat-Miyah |
| Maybrat Suruwan | ayz | 44 | Proto-Maybrat-Miyah |
| Maybrat Sira | ayz | 46 | Proto-Maybrat-Miyah |
| Maybrat Seni | ayz | 3 | Proto-Maybrat-Miyah |
| Maybrat Sejá | ayz | 1 | Proto-Maybrat-Miyah |
| Maybrat Sawin | ayz | 48 | Proto-Maybrat-Miyah |
| Maybrat Northern | ayz | 39 | Proto-Maybrat-Miyah |
| Maybrat Mogetemin | ayz | 118 | Proto-Maybrat-Miyah |
| Maybrat Marā | ayz | 2 | Proto-Maybrat-Miyah |
| Maybrat Mare | ayz | 175 | Proto-North Maybrat-Miyah |
| Maybrat Lacustrine | ayz | 4 | Proto-Maybrat-Miyah |
| Maybrat Kotjuwer | ayz | 2 | Proto-Maybrat-Miyah |
| Maybrat Kauf | ayz | 7 | Proto-Maybrat-Miyah |
| Maybrat Karmangani | ayz | 47 | Proto-Maybrat-Miyah |
| Maybrat Karet Tubun | ayz | 49 | Proto-Maybrat-Miyah |
| Maybrat Kami | ayz | 48 | Proto-Maybrat-Miyah |
| Maybrat Kambuaya | ayz | 240 | Proto-Maybrat-Miyah |
| Maybrat Jiu | ayz | 1 | Proto-Maybrat-Miyah |
| Maybrat Jitmare | ayz | 95 | Proto-North Maybrat-Miyah |
| Maybrat Fuok | ayz | 1 | Proto-Maybrat-Miyah |
| Maybrat Framesá | ayz | 16 | Proto-Maybrat-Miyah |
| Maybrat Fan | ayz | 49 | Proto-Maybrat-Miyah |
| Maybrat Erokwero | ayz | 189 | Proto-Maybrat-Miyah |
| Maybrat Eastern | ayz | 31 | Proto-Maybrat-Miyah |
| Maybrat East Ayfat Senopi | ayz | 40 | Proto-Maybrat-Miyah |
| Maybrat East Ayfat | ayz | 185 | Proto-Maybrat-Miyah |
| Maybrat Ayawasi | ayz | 1217 | Proto-Maybrat-Miyah |
| Maybrat Ayamaru | ayz | 1057 | Proto-Maybrat-Miyah |
| Maybrat Arné | ayz | 1 | Proto-Maybrat-Miyah |
| Maybrat Aitinyo | ayz | 412 | Proto-Maybrat-Miyah |
| Maybrat | ayz | 2132 | Proto-Maybrat-Miyah |
| Matbat | xmt | 1180 | Proto-Maya-Matbat |
| Marau | mvr | 8 | Proto-West Yapen Nuclear |
| Mansim | | 463 | Proto-Hatam-Mansim |
| Manombai Wokam | woo | 321 | Proto-Southern Aru |
| Manombai | woo | 77 | Proto-Southern Aru |
| Mairasi | zrs | 209 | Proto-Mairasi |
| Maba | mqa | 1061 | Proto-Central-Eastern South Halmahera |
| Loloda | loa | 1410 | Proto-Loloda |
| Lamaholot Solor | slp | 1319 | Proto-Flores-Lembata |
| Kurudu | kjr | 742 | Proto-East Yapen |
| Kur | kuv | 50 | Proto-Teor-Kur |
| Konda Dema | knd | 119 | Proto-South Bird's Head |
| Konda | knd | 384 | Proto-South Bird's Head |
| Kokoda Tarof | xod | 130 | Proto-South Bird's Head |
| Kokoda Negeri Besar | xod | 494 | Proto-South Bird's Head |
| Kokoda Nayarago | xod | 92 | Proto-South Bird's Head |
| Kokoda Kasueri | xod | 600 | Proto-South Bird's Head |
| Koiwai | kwh | 283 | Proto-Koiwai-Irarutu |
| Kesui Temertimer | | 60 | Proto-Seram Laut |
| Kemberano Weriagar | bzp | 404 | Proto-South Bird's Head |
| Kemberano Kalitami | bzp | 160 | Proto-South Bird's Head |
| Kemberano Bomberai | bzp | 235 | Proto-South Bird's Head |
| Kemberano Barau | bzp | 174 | Proto-South Bird's Head |
| Kei Doulan | kei | 34 | Proto-Kei-Tanimbar |
| Kei | kei | 342 | Proto-Kei-Tanimbar |
| Kalamang Mas | kgv | 50 | Proto-Greater West Bomberai |
| Kalamang Karas Laut | kgv | 28 | Proto-Greater West Bomberai |
| Kalamang | kgv | 2852 | Proto-Greater West Bomberai |
| Kalabra Kuwani | kzz | 78 | Proto-Tehit |
| Kalabra Beraur | kzz | 113 | Proto-Klabra-Salkma |
| Kalabra | kzz | 377 | Proto-Klabra-Salkma |
| Kais Kampung Baru | kzm | 350 | Proto-South Bird's Head |
| Kais | kzm | 166 | Proto-South Bird's Head |
| Kadai | kzd | 566 | Proto-Saluan-Banggai |
| Kaburi Kambor | uka | 150 | Proto-South Bird's Head |
| Kaburi Benawa | uka | 82 | Proto-South Bird's Head |
| Irires Akmuri | | 40 | Proto-East Bird's Head |
| Inanwatan Solowat | szp | 48 | Proto-South Bird's Head |
| Inanwatan Samalek | szp | 119 | Proto-South Bird's Head |
| Inanwatan Robabuan | szp | 46 | Proto-South Bird's Head |
| Inanwatan Giruri | szp | 48 | Proto-South Bird's Head |
| Inanwatan Gemor | szp | 47 | Proto-South Bird's Head |
| Inanwatan Bira | szp | 47 | Proto-South Bird's Head |
| Inanwatan Besam | szp | 46 | Proto-South Bird's Head |
| Inanwatan | szp | 1717 | Proto-South Bird's Head |
| Iha Wayati | ihp | 167 | Proto-Mbaham-Iha |
| Iha Tetar | ihp | 48 | Proto-Mbaham-Iha |
| Iha Sum | ihp | 48 | Proto-Mbaham-Iha |
| Iha Sipatnanam | ihp | 62 | Proto-Mbaham-Iha |
| Iha Pikpik | ihp | 18 | Proto-Mbaham-Iha |
| Iha Nambuktep | ihp | 32 | Proto-Mbaham-Iha |
| Iha Kapaur | ihp | 278 | Proto-Mbaham-Iha |
| Iha Degen | ihp | 47 | Proto-Mbaham-Iha |
| Iha Danaweria | ihp | 47 | Proto-Mbaham-Iha |
| Iha | ihp | 1478 | Proto-Mbaham-Iha |
| Idate | idt | 667 | Proto-Timor-Babar |
| Hewa | | 739 | Proto-Flores-Lembata |
| Hatam | had | 77 | Proto-Hatam-Mansim |
| Gorontalo | gor | 89 | Proto-Gorontalo |
| Gorom | | 77 | Proto-Seram Laut |
| Geser Waru | ges | 919 | Proto-Seram Laut |
| Gebe | gei | 1165 | Proto-Central-Eastern South Halmahera |
| Gane Wosi | gzn | 114 | Proto-Southern South Halmahera |
| Gane Saketa | gzn | 116 | Proto-Southern South Halmahera |
| Gane Dalam-Luar | gzn | 122 | Proto-Southern South Halmahera |
| Gane | gzn | 839 | Proto-Southern South Halmahera |
| Galela | gbi | 1050 | Proto-Galela |
| Fataluku Vialo | ddg | 32 | Proto-FRATA |
| Fataluku Central | ddg | 1163 | Proto-FRATA |
| Etskebi Akari | | 39 | Proto-East Bird's Head |
| Erokwanas Goras | erw | 52 | Proto-East Bomberai |
| Erokwanas Darembang | erw | 24 | Proto-East Bomberai |
| East Makian Tahane | mky | 111 | Proto-Southern South Halmahera |
| East Makian Soma | mky | 110 | Proto-Southern South Halmahera |
| East Makian Peleri-Samsuma | mky | 112 | Proto-Southern South Halmahera |
| East Makian Ngofakiaha | mky | 114 | Proto-Southern South Halmahera |
| East Makian Ngofagita | mky | 113 | Proto-Southern South Halmahera |
| East Makian Mailoa | mky | 110 | Proto-Southern South Halmahera |
| East Makian Kayoa | mky | 113 | Proto-Southern South Halmahera |
| East Makian | mky | 1186 | Proto-Southern South Halmahera |
| Dusner | dsn | 363 | Proto-Biakic |
| Duriankari Sisir Beyun | dbn | 119 | Proto-South Bird's Head |
| Duriankari | dbn | 38 | Proto-South Bird's Head |
| Dobel | kvo | 1167 | Proto-Southern Aru |
| Dengka | dnk | 22 | Proto-Western Rote |
| Central Asmat | cns | 7941 | Proto-Asmat-Kamoro |
| Busami | bsm | 38 | Proto-West Yapen Nuclear |
| Buol | blf | 599 | Proto-Buol-Gorontalo |
| Buli | bzq | 1084 | Proto-Central-Eastern South Halmahera |
| Biga | bhc | 92 | Proto-Raja Ampat |
| Biak Numfor | bhw | 107 | Proto-Nuclear Biakic |
| Biak | bhw | 1254 | Proto-Nuclear Biakic |
| Bedoanas Forir | bed | 47 | Proto-East Bomberai |
| Bedoanas Andamata | bed | 51 | Proto-East Bomberai |
| Batuley | bay | 1336 | Proto-Southern Aru |
| Banda | bnd | 292 | Proto-Banda |
| Bajau Kayoa | bdl | 110 | Proto-Sama-Bajau |
| Bacan Malay | btj | 110 | Proto-Malay |
| As | asz | 192 | Proto-Raja Ampat |
| Arguni | agf | 387 | Proto-East Bomberai |
| Arandai | jbj | 299 | Proto-South Bird's Head |
| Ansus | and | 333 | Proto-West Yapen Nuclear |
| Anason Akmuri | | 40 | Proto-East Bird's Head |
| Amarasi Kupang | aaz | 22 | Proto-Meto |
| Abun Ye | kgr | 116 | Proto-Abun |
| Abun Tat | kgr | 190 | Proto-Abun |
| Abun Sausapor | kgr | 219 | Proto-Abun |
| Abun Mega | kgr | 43 | Proto-Abun |
| Abun Madik | kgr | 259 | Proto-Abun |
| Abun Ji | kgr | 193 | Proto-Abun |
| Abun Arapi | kgr | 40 | Proto-Abun |
| Abun | kgr | 315 | Proto-Abun |