Molluscs have a wide variety of sexual systems and have undergone many transitions from separate sexes to hermaphroditism or vice versa, which is of interest for studying the evolution of sex determination and differentiation. Following the serendipitous observation that sex was the primary driver of genetic structure in the hydrothermal vent gastropodAlviniconcha boucheti, we investigated sexual systems and sex determination in this species and two others of the same genus. We combined genome-wide multi-locus genotypes obtained from RAD sequencing with anatomical observations of the gonads of the threeAlviniconchaspecies occurring in the southwest Pacific Ocean:A. boucheti(n=207),A. strummeri(n=41 ind.) andA. kojimai(n=251). In two of the species (A. bouchetiandA. strummeri), the sexes are separate and genetically determined by a male-heterogametic (XY) system. External observation of the gonads in the third species (A. kojimai) also suggested that the sexes were separate, but histological analyses revealed that 76% of the individuals classified as females from external observation of the gonads presented a mosaic of male and female reproductive tissue. Empirical analyses and simulations showed nonetheless that 14 RAD loci were sex-linked with an XY signature inA. kojimai(as compared with 64 inA. strummeriand 373 inA. boucheti). Comparison across species and mapping of RAD loci to a non-contiguous reference genome assembly of the related speciesA. marisindicashowed that all sex-linked loci identified inA. kojimaiare located on five scaffolds that also contain 25 and 73 sex-linked RAD loci in the other two species, respectively. These results suggest that all threeAlviniconchaspecies share the same XY sex determination system, but that the gonad of XXA. kojimaiindividuals are invaded by a variable proportion of male reproductive tissue. It remains to be seen whether the male tissue in these intersex individuals is functional or not. This situation of three species showing variation in gonadal development around a probably common sex determination system provides new insights into the reproductive mode of poorly known deep-sea species and questions the evolution of gametogenetic polymorphism in these species.