Several species of molluscan bivalves have a peculiar mode of mtDNA transmission, known as doubly uniparental inheritance (DUI). In these species, two mitochondrial genomes, M-type mtDNA and F-type genomes, coexist in stable state. In this study, the cDNA sequence of M and F-type COII gene of H.cumingii was cloned by RACE, QRT-PCR was used to study the expression of M and F -type COII genes in H.cumingii at different stages. We found that (i) The full-length cDNA sequence of the M-type is 1244 bp; and F-type COII is 808 bp, the C-terminus extension to the M-type COII protein has four transmembrane regions confirming that the extension is functional (ii) M-type COII gene and F-type COII gene were all expressed in gonad tissues from embryos to 5-month-age old H.cumingii, and the expression level of F-type COII gene in the same period was significantly higher than that of M-type COII gene. (iii) In semi-age old H.cumingii, F-type mtDNA was expressed mainly in somatic tissues and little in gonads, while M type expressed mainly in gonads and little in somatic tissues; (iv) In one-age old H.cumingii, F and M type both expressed in female somatic tissues and gonads, while in males F type expressed in all tissues and M type only expressed in gonads; (v) In two-age old H.cumingii, F type was