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Historical populated place (A populated place that no longer exists)
| name | alternatenames | latitude | longitude | timezone | modification_date |
| San’ya | San'ya,San’ya | 35.71667 | 139.8 | Asia/Tokyo | 2016-06-22 |
| Ōi-Minamihamagawachō | 35.6 | 139.73333 | Asia/Tokyo | 2016-06-22 | |
| Nihombashi-Edobashi | Edobashi,Nihombashi-Edobashi | 35.68333 | 139.76667 | Asia/Tokyo | 2016-06-22 |
| Mikawashimachō | Mikawashima,Mikawashimacho,Mikawashimachō,Mikawashimamachi | 35.73333 | 139.78333 | Asia/Tokyo | 2016-06-22 |
| Fukayachō | Fukaya,Fukayacho,Fukayachō,shen gu ding,深谷町 | 36.2 | 139.28333 | Asia/Tokyo | 2017-04-09 |
| Azabu-Fujimichō | Azabu-Fujimicho,Azabu-Fujimichō,Fujimicho,Fujimichō | 35.65 | 139.73333 | Asia/Tokyo | 2016-06-22 |
| Amarume (now Shonai) | Amarume,Ar-arume,yu mu,余目 | 38.84461 | 139.90348 | Asia/Tokyo | 2017-04-09 |
| Moji | 33.94667 | 130.96589 | Asia/Tokyo | 2018-12-12 | |