Different groups of microorganisms in a two-phase anaerobic system were enumerated to evaluate the prevalence of specific groups and species. Total and fecal coliforms showed similar values both in acidogenic and methanogenic reactors. The fecal streptococci were 4-fold higher in the acidogenic reactor, when compared with those of the methanogenic reactor. As expected, no methane forming or sulfate reducing bacteria were found in the acidogenic reactor. The populations of methanogenic bacteria were dominated by a mixed population of straight to curved rods and multicellular filaments which strongly resembled members of the genus Methanosaeta. Seven prevalent species of facultative anaerobic gram-negative bacteria were identified as Previdencia alcalifacienciens, Providencia rettgeri, Enterobacter cloaceae, Citrobacter freundii, Klebsiella oxytoca, Proteus pennri and Yersinia enterocolitica. The species Pseudomonas aeruginosa, Stentophomonas maltophila and Acinotobacter iwoffi, were the most frequently isolated glucose non-fermenting gram-negative bacilli. Among these species, only P. aeruginosa was present in high number in each sample.