The over-exploitation of fishery resources, by-catch, destruction of marine environment, pollution and global change resulted in the reduction in biodiverstity of fish. The research of biodiversity of fish is extremely urgent and the investigation of fish species is the first step. This study is to recheck the fish samples in hand and to investigate in the biodiversity of fish in the eastern waters of Taiwan. This study recoded a total number of 41 families and 139 species of intertidal fishes in 2008~2009. Record 856 species for fishes in the eastern waters of Taiwan was arrayed in the past, the intertidal fishes account for 16.2%.This study recoded a total number of 73 families and 358 species of subtidal zone eastern coast fishes in 2010. Record 856 species for fishes in the eastern waters of Taiwan was arrayed in the past, the subtidal fishes account for 41.8%. This study will recod estuary and migratory fishes in this year. Further, a database of name list for fishes in theeastern waters of Taiwan will be established. The result of the study could be applied to the education of biodiversity of fish and form the basis of sustainable utilization of fishery resources.