Climate change in conjunction with other human impacts, may ultimately rearrange the global distribution of marine life. To detect the distortion of ecosystem, it becomes indispensable to monitor not only some target species but also whole community. Taiwan is located at a complex convergent boundary between the Philippine Sea Plate and the Eurasian Plate, and Kuroshio current runs through the surrounding ocean. By analyzing the samples from the trawl-net surveys registered in the Fish Database of Taiwan and the monthly monitoring data at the nuclear power plants in northern Taiwan, we estimate the α,β,γ- genetic diversity of the fish community. The database includes 642 species in western Taiwan (10-800m below sea surface), 376 species in eastern Taiwan (140-3,879m), and 332 species in northern Taiwan. We averaged the COI distances as genetic diversity of 387 targeted fish communities. The low value of the β diversities of coastal pelagic fish may be due to high gene flow. The communities of bathypelagic fish had high γ diversities. The samples from the deep-sea are smaller than the others. This may be the cause of the small value of α diversity and large value of β diversity of the community.