Insight into the influence of UV-C radiation on the evolutionary relationship between prokaryotic and eukaryotic algae was studied in seven species of algae exposed to different UV-C irradiances. The order of their acclimation (from most tolerant to sensitive) is Synechococcus sp. PCC7942 (Cyanophyta), Synechocystis sp. PCC6803 (Cyanophyta), Chlorella protothecoides (Chlorophyta), Chlamydomonas reinhardtii (Chlorophyta), Phaeodactylum tricornutum (Bacillariophyta), Alexandrium tamarense (Pyrrhophyta) and Dicrateria zhanjiangensis (Chrysophyta). These results are in accordance with the algal evolution process that is generally accepted and proved by fossil record. It shows that UV-C radiation is an important environmental factor that cannot be ignored in the evolutionary process from prokaryotic algae to eukaryotic algae. The threshold of UV-C radiation at which prokaryotic algae can survive but eukaryotic algae cannot was found to be approximately 0.09 W m−2. This was the first time to determine with precision the irradiance level at which UV-C contributed as a selection pressure of evolution. Furthermore, the effects of UV-C radiation on photosynthetic performance, growth rate and pigment content were investigated in two species of prokaryotic algae: Synechococcus sp. PCC7942 and Synechocystis sp. PCC6803, and two species of eukaryotic algae: C. reinhardtii and C. protothecoides. After 6 days of exposure, the contents of chlorophyll a and carotenoids decreased in all species, moreover reduction in C. reinhardtii and C. protothecoides was more obvious than in Synechococcus sp. PCC7942 and Synechocystis sp. PCC6803. The ability to photosynthesize followed the same trend as the pigments.