Some small basins have developed in the northern Philippine Sea along the northern and southern sides of the Daito Ridge (DR): the Kita-Daito Basin (KDB), Amami-Sankaku Basin (ASB) and Minami-Daito Basin (MDB). From the interpretation of multichannel reflection seismic profiles crossing these basins, their noticeable differences of geological character can be recognized. There are several E–W trending normal faults in the main part of the KDB which suggest that this basin was formed by seafloor spreading. A seismic section crossing the Oki-Daito Ridge (ODR) and DR presents a reflector, possibly indicating subduction of the slab containing the ODR. The subduction probably caused back-arc spreading of the KDB, which finally ceased upon the collision of both ridges. Based on the trace of characteristic reflectors in seismic sections and correlations with several drill holes, sediments are divided into Units I through V, ranging from Lower Eocene to Holocene. The Choju Seamounts occupy the middle part of the MDB, dividing the basin into the eastern main basin and the western small subbasin (Minami-Daito Nishi Sub Basin; MDNSB). The seismic character of Unit II (≒ Middle to Upper Eocene) is noticeably different among the ASB, the main basin of MDB, and the MDNSB, indicating different sources of sediments. The thickness of Unit II in the ASB increases towards the Kyushu-Palau Ridge (KPR), indicating that sediments were supplied by the KPR. Unit II in the main basin of MDB has no direct relationship with the KPR, and should have had another source, such as the DR or the ODR. The thickness of Unit II in the MDNSB increases towards the DR, suggesting an equivalent origin of the carbonate layer at the top of the DR.