The complex and diverse sexual reproduction patterns and multiple sex types of mollusks make it important to elucidate their sex mechanisms. Recent studies have demonstrated the crucial roles of Dmrt, STAT, and Sox genes in animal sex determination/differentiation. However, the comprehensive comparison of these genes in different bivalves is limited. In this study, 33 bivalves were analyzed to investigate the sequence characteristics, phylogenetic relationships, and expression profiles of these genes. Total of 112 Dmrt genes, 88 STAT genes and 229 Sox genes were identified in 33 bivalves. Phylogenetic analysis grouped the Dmrt, STAT, and Sox genes into 4, 3, and 7 groups, respectively. By comparing gene family number and sequence differences, we observed expansion and contraction in the Dmrt and STAT family genes, as well as sequence variations in Dmrt-01 and SoxH among different bivalves, suggesting their molecular adaptations to diverse sexual mechanisms. Expression profiles of these genes in noble scallop Chlamys nobilis revealed that CnDmrt-01 and CnSox-07 (SoxH) is predominantly expressed in testis, suggesting their male-specific role in gonad development and maturation. A higher expression level of CnSox-01/03 (Sox-B1/C) in ovary suggest their essential role in ovary development. These genes also showed significantly higher expression level during sex reversal, suggesting their crucial roles in this process. Additionally, transcriptome data from other bivalves further support that the sexual expression patterns of Dmrt-01 and Sox-B1/C/H are conserved across most bivalves. The results of this study will provide insights into these sex-related genes and useful information to better understand mechanisms of gonad development and sex reversal in mollusc.