Abstract: In the fields of evolutionary ecology, evolutionary biology and cell biology, symbiosis between Hydra sinensis and single-celled green algae is a special biological phenomenon with high scientific value. Although the biological significance of hydra-algea has been understood, its origin and evolutionary mechanism are still unclear by now. In the hydra-algae symbiosis status, free living algae goes into its host cell during evolution, so the study on the origin of symbiotic algae can help understand the mechanism of hydra-algae symbiosis. In this study, 18S rRNA gene sequences in nucleolus and nine protein-coding genes (atpA, chlB, chlN, petA, psaB, psbA, psbC, psbD and rbcL) in chloroplast were cloned and sequenced from the symbiotic green algae in H. sinensis. With the application of Maximum Likelihood (ML) and Bayesian analysis methods, the significance of phylogenetic of the unicellular green algae endosymbiotic in H. sinensis was examined. The results show that the endosymbiotic green alga are belong to Chlorellales, Trebouxiophyceae, instead of Chlorellal; the green alga in paramecium, hydra, lichen and ginkgo are belong to Trebouxiophyceae, whereas others from frog and salamander are in Chlorophyceae. However, these two groups of endosymbiotic alga could live in the same host without forming a monophyletic group. In addition, endosymbiotic alga from different host cells have different origins.