Genetic divergence between non-scaly form and scaly form of pen shell Atrina pectinata (Linne) was examined. Isozyme analyses indicated replacement of major alleles at the AAT^*, CK-1^*, GPI-1^*, GPI-2^*, LAP^*, MDH^*, MPI^* and PGM^* loci, and difference of allele frequency at the GAPDH^* loci. Heterozygosity histogram of scaly form indicated a bimodal distribution, some individuals of the scaly form had many heterozygotes at the diagnostic loci. The obsevation that the shell morphology of the individuals showed intermediate state between non-scaly and scaly form suggested that they were hybrids between the two forms. The genetic distance (D value) between the two forms, calculated from isozymic allele frequencies, was 0.469, a figure significant at the inter-specific level. The considerable genetic difference and the presence of low frequency of hybrids in a sympatric population suggested that the two forms are distinct species. Morphologically, since the two forms could be completely distinguished by presence of the squamation, the two forms should be taxonomically distinguished.
