16S rDNA sequences of strains of Rhodoferax fermentans were analyzed and compared with those of species of the genera Rubrivivax and Rhodocyclus. Approximately 1.5-kb fragments of 16S rDNA from crude cell lysates were amplified by the polymerase chain reaction (PCR) and sequenced directly by using Tth DNA polymerase with the linear PCR sequencing protocol, followed by on-line detection with an automated laser fluorescent DNA sequencer. Pairwise sequence comparisons and distance matrix tree analysis showed that Rhodoferax fermentans, Rubrivivax gelatinosus, and Rhodocyclus species belong to three separate lineages within the beta subclass of the Proteobacteria, thereby confirming the phylogenetic validity of the genus Rhodoferax, as well as of the genera Rubrivivax and Rhodocyclus.