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In a taxonomic study of the known Pediococcus species, together with 116 isolates from fermenting tef dough and fermented kocho using a PCR-based RAPD procedure, all the different species developed well differentiated agarose gel electrophoresis profiles. Analyses of the images with the Pearson product moment correlation coefficient (r) and UPGMA clustering algorithm in the GelCompar version 4.0 software gave a distinct identification scheme within and between type strains and food isolates of Pediococcus species. The procedure is simple, rapid for grouping of isolates, applicable to all species of pediococci and particularly useful for differentiating between strains of Ped. pentosaceus and Ped. acidilactici.