Since some cyanobacterial isolates under selective culturing conditions are lacking of characteristic specialized cells or showing altered morphology, the morpho-taxonomic criteria are not accurate enough to discriminate between species. Instead of morphological parameters, a method based on the single or the combination of repetitive oligonucleotides in a single PCR, repetitive oligonucleotides-primed PCR (ROP-PCR), was applied to generate DNA profiles for members of the cyanobacterial genera Anabaena and Oscillatoria, both of which are responsible for causing poisonous blooms in various freshwater systems. ROP-PCR performed on 10 isolates of the cyanobacteria with ERIC and REP sequences from gram-negative bacteria, STRR1A and LTRR sequences derived from cyanobacterial genome, and eukaryotic repetitive sequences, led to the identification of distinct genotypes, and provided specific and repeatable DNA fingerprints for cyanobacterial isolates. Grouping analysis of cyanobacterial isolates showed a signifiant difference depending on the primer used in PCR.