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A molecular system was developed and tested to efficiently analyze algal communities in river water samples. Polymerase Chain Reaction (PCR) primers were designed to amplify the 18S rRNA gene of certain taxonomic groups of freshwater algae; there was limited success in specific amplification. Additionally, a primer pair utilizing both the 16S plastid gene and the 16S rRNA gene was tested with success, amplifying both prokaryotic and eukaryotic algae while excluding other taxonomically similar organisms. The terminal restriction fragment length polymorphism (TRFLP) fingerprinting method, which has been used in previous studies to examine prokaryotic community structure, was modified with the successful algae primers to selectively fingerprint all algal groups in two San Joaquin River water samples. Triplicates of two TRFLP profiles have been generated and terminal restriction fragments (TRFs) have been assigned to specific algal species.