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Spectral absorption method based on two step linear regression analyses (TSLR) was applied for detection of two strains of cyanobacterium, Microcystis (blue-green algae) from eukaryotic algae. Both blue-green algae, algae and dissolved organic carbon (DOC) were considered from freshwater bodies in Kanto region, Japan. The results show that blue-green species can be detected from other algal species using absorption spectra of water samples. In this study statistical analysis was done by TSLR method, which determined the gradient vectors of single algal species and DOC. We believe that this method might be useful in environmental monitoring of freshwater algae.