Although spirochetes were first detected in crystalline styles of bivalves more than 100 years ago, little is known about the characteristics of these consortia (commensalism or parasitism). The presence of spirochetes in bivalves can so far not be generalized. The purpose of this study was the detection and phylogenetic identification of spirochetes associated with crystalline styles of different marine bivalve species collected in temperate regions and Antarctica. Polymerase chain reaction amplification of spirochete 16S ribosomal gene sequences was performed. 16S ribosomal gene clones were identified by phylogenetic analysis, and the variability within each bivalve species was determined. The spirochetes were mainly related to yet uncultured or potentially pathogenic spirochetes from the marine environment. All identified spirochete clones fell into 2 families: the Spirochaetaceae with 2 genera, Cristispira and Spirochaeta, and the Brachyspiraceae, with the genus Braehyspira. The diversity of spirochetes in the crystalline style of each bivalve species was low. All clone sequences from crystalline styles of the oyster Crassostrea gigas clustered into the group of Cristispira species. Interestingly, these Cristispira spirochetes were previously found in Crassostrea virginica, another oyster species. The spirochete clones of each bivalve species formed distinct clusters. We therefore assume that the investigated bivalve species harbor distinct populations of spirochetes. Although spirochetes were not found in all the investigated samples, the occurrence of spirochetes was not random and implies a closer association between the bivalve species and the specific spirochete cluster.