DNA analysis was conducted on the dominant species of microalgal culture under the LEDs irradiating condition. The results showed that diatoms and dinoflagellates were detected when the light source was only sunlight, whereas sunlight + LED (blue+red) condition showed that the proportion of eukaryotic algae increased dramatically, and green algae and diatoms, crypto algae dominated. Under each condition irradiated with the blue or red LED, all the clones under the red LED are closely related to the Synechococcus species. Under the blue LED, the diatoms (closely related species such as Chaetoceros genus) were dominated. These results were suggested that red LEDs promote dominance of blue-green algae, and blue LEDs tend to promote dominance of diatom species. In addition, cyanobacterial clones dominated by red LEDs are closely related to toxin-producing strains and concerned about toxicity. On the other hand, the majority of diatom clones dominated by blue LEDs were closely related to useful species used as food for aquaculture and the like.