We have tested a set of oligonucleotide primers originally developed for the specific amplification of 16S rRNA gene segments from cyanobacteria, in order to determine their versatility as an identification tool for phototrophic eucaryotes. Using web-based bioinformatics tools we determined that these primers not only targeted cyanobacterium sequences as previously described, but also 87% of sequences derived from phototrophic eucaryotes. In order to qualify our finding, a type culture and environmental strain from the freshwater unicellular, green algae genus Chlorella Beijerinck, were selected for further study. Subsequently, we sequenced a 578-bp fragment of the 16S rRNA gene, which proved to be present within the chloroplast genome, performed sequence analysis and positively identified our solvent-degrading environmental strain (SDC1) as Chlorella vulgaris.