The study area named Bonin basin is located in the northeast Philippine sea. This paper addresses the radiolaria stratigraphy of Late Eocene-Quaternary sediments. The materials were collected from 782A Hole, Ocean Drilling Program, Leg 125. Based on the biozonation by Sanfilippo et al. in 1985, ten fossil zones are divided. Zones Stichocorys wolffii-Lychnocanoma elongata and Didymocyrtis antepenultima are missing. The two hiatuses are detected as follows: between Late Oligocene/late Early Miocene. Middle Miocene/Late Miocene. The five boundaries are as follows: Eocene/Oligocene, Oligocene/Miocene, Middle Miocene/Late Miocene, Miocene/Pliocene and Tertiary/Quaternary. Most of the Quaternary radiolaria in this studied area are warm water species. In this area, fossil abundance and diversity are lower than those in the tropical latitude. Several cold water species are paragenetic with them, and fossil abundance is large, so in the studied middle latitude area they maybe distribute in shallower water. From the change of radiolaria simple diversity, we can identify five relative warmer water stages and five relative colder water stages from Miocene to Quaternary. Oligocene is a colder water stage. The result is in accord with the change of nannofossil complex diversity and the content of calcium carbonate in hole 782A. The hiatus between Late Oligocene/Early Miocene may be formed by the violent scouring of bottom currents. It may be caused by the extension of the Antarctic ice cap in Miocene.