Nitrogen-fixing Acetobacter diazotrophicus, Herbaspirillum seropedicae and Herbaspirillum rubrisubalbicans colonize sugar cane, and are thought to be capable of supplying high levels of fixed nitrogen to this plant. Eight A. diazotrophicus, two H. seropedicae and four H. rubrisubalbicans isolates were identified and compared by complementary biochemical and genetic methods. Utilization of carbon sources and antibiotic resistance patterns allowed differentiation of A. diazotrophicus from Herbaspirillum species. In order to distinguish strains within A. diazotrophicus species, the polymerase chain reaction was employed, using a Rhizobium melilotidctA primer under low stringency hybridization conditions.