The Vestimentifera, or deep-sea tube worms, comprise an ecologically and anatomically unusual group of marine invertebrates, with poorly understood biogeography, ecology, phylogenetic affinities and evolutionary radiation. To gain insight into evolutionary diversification within the group, we have used a molecular biological approach. We report the cloning of a region of 28S ribosomal DNA from representatives of five vestimentiferan genera plus, for comparison, a polychaete and a perviate pogonophore. Phylogenetic analyses using these DNA sequences confirm that Ridgeia and Tevnia are closely related genera. The analyses also lead us to propose the hypothesis that the earliest vestimentiferan lineage to diverge gave rise to the genus Lamellibrachia only. In addition, our comparative DNA sequence data now provide a means to use molecular methods for identification of deep-sea tube worms; we employed this approach to demonstrate that the first vestimentiferan specimen from the eastern Atlantic Ocean belongs to the genus Lamellibrachia. DNA-based identification should have wide applications in the study of vestimentiferan biogeography and ecology.