Seed production of cultured aquatic organisms is one of the most important issues forsustainable aquaculture industry in Taiwan. The culture collection center of live food isbuilt up to provide stock cultures and relative technology for farmers and researchers.Ten culture collections of Chlorella had different EPA content in lipid, showed there arenot the same species. It is difficult to identify due to small size (< 5 μm), ovoid shape,without features on cell cover. To determine the relationships among Chlorella spp.strains, the PCR technique to analyze the nuclear-encoded SSU 18S rDNA sequencewill be used. In addition, this study is aimed to establish the technique for phylogeny ofmicroalgae culture collection.