Symbiotically associated cyanobacteria from 18 accessions within all known species in the genus Azolla were examined and classified by the use of polymerase chain reaction (PCR)-fingerprinting. A repetitive sequence specific for cyanobacteria, the short tandemly repeated repetitive (STRR) sequence, was used as a primer in the reaction. Cyanobacterial filaments isolated directly from the Azolla leaf cavity or contained within homogenised symbiotic Azolla tissue were used as templates. Based on the fingerprint pattern, distinct differences were demonstrated between cyanobacteria isolated from the Euazolla and Rhizosperma sections. In addition, individual fingerprints were obtained from all cyanobacteria isolated from the different Azolla species. The fingerprints were used to generate a phylogenetic tree. Three clusters were distinguished: one contained the four isolates from the section Euazolla, a second the isolate from Azolla filiculoides, and a third the three isolates from the section Rhizosperma. By the use of STRR-PCR fingerprinting, new data on the taxonomy of cyanobacteria in Azolla were obtained, which have been difficult to generate by other classification methods. PCR-fingerprinting may, therefore, be a valuable tool for diversity and classification studies of symbiotic cyanobateria from Azolla and, as co-evolution between the cyanobacteria and its corresponding host exists the method may also be useful for the taxonomy of Azolla.