Thalassospira bacteria are now found ubiquitous in marine environments, hi this report, fifty-seven strains isolated from seawater and deep sea sediment sampled at 31 sites were subjected to phylogenetic analysis, based on sequences of 16S rRNA, gyrB and ropD genes, as well as the fingerprint of BOX-PCR. As a result, 16S rRNA gene was highly conserved with exception only a few variable regions, hi contrast, the gyrB and rpoD gene sequences were highly variable. The comparison of the BOX-PCR fingerprint, gyrB and ropD phylogenetic trees revealed a similar branch topology with that of the 16S rRNA gene. But deeper-branches were found in the BOX-PCR fingerprint, gyrB and ropD phylogenetic trees. This suggests that the BOX-PCR analysis, rpoD and gyrB genes were useful complementary phylogenetic markers for investigation of evolutionary relationships among Thalassospira species. The results provide evidences about the diversity of Thalassospira species and contribute to a better comprehension of their adaptation in various marine environments.