Bindin is a major protein packaged as insoluble granules in sperm acrosomes. It may be responsible for speciesspecific recognition and binding of sperm to a glycoprotein receptor on the surface of eggs. The putative functional region of bindin is a fucose-binding lectin (F-lectin) domain. We cloned a novel bindin gene from the Kumamoto oyster Crassostrea sikamea by 3′ and 5′ RACE. The full-length cDNA of C. sikamea bindin was 1,134 bp, with a 774-bp open reading frame encoding 257 amino acids. The deduced amino acid sequence contained a putative signal peptide of 24 amino acids. The length of the bindin genomic DNA we obtained was 5,353 bp, containing 4 exons and 3 introns. We studied F-lectin repeats of the bindin gene from 3 species of Crassostrea to detect the relationship between them and found 11,2, and 5 haplotypes from C. sikamea, Crassostrea angulata, and Crassostrea gigas, respectively. Phylogenetic trees showed a closer relationship between C. gigas and C. angulata than between C. gigas and C. sikamea. Two haplotypes of C. angulata fell into 2 different clades, one in the C. gigas clade and the other in the C. sikamea clade. Deduced amino acid sequences and hydropathy plots were considerably similar among these species, indicating the close resemblance in the tertiary structure of bindin proteins. To test for selection, we compared the number of nonsynonymous substitutions and synonymous substitutions per nucleotide site among the 18 F-lectin haplotypes. This analysis identified 7 positively selected positions (P> 95%) among 18 haplotypes from the 3 species, all located on the F-lectin binding face around the 3 residues that are specifically involved in binding fucose (H37, R64, and R70). We hypothesize that these 7 clustered amino acids may be related to species recognition and thus could impose selective pressure on bindin divergence.