The genus Rubritalea contains a number of environmental species and cultured species which are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the phylogenetic relationships of all known species and six new isolates of the genus Rubritalea were investigated by analyzing the sequence of gyrB, a gene that encodes the B subunit protein of DNA gyrase. Results from sequence analysis demonstrated that the interrelationships inferred from the gyrB gene-based phylogeny showed better resolution than those based on their 16S rRNA gene sequences for the differentiation of strains at the species level. Moreover, the genomic DNA-DNA relatedness values and differential chemotaxonomic data also supported the results of gyrB gene-based phylogeny. It is concluded that the gyrB could be used as a suitable gene marker for close relationships of the Rubritalea group within the phylum ‘ Verrucomicrobia’.