Abstract The diverse modes of sexual reproduction in Bivalvia make it an excellent clade to understand the evolution of sex and sex determination. The cosmopolitan Pacific oyster Crassostrea gigas is an ideal model for bivalve sex determination studies because of its complicated sexuality, including dioecy, sex change and rare hermaphroditism. A major barrier to C. gigas sex determination study has been the lack of information on the type of sex determination. To identify its sex-determining system, sex observation by following the same individual in two consecutive years was conducted on 760 oysters from distinct populations. Stable sexuality and sex reversal in both directions were observed, which provides a case against the protandry of C. gigas. Restriction site-associated DNA sequencing (RAD-seq) based on 26 samples with unchanged and converted sexualities was carried out for identifying sex-linked marker. One SNP Cgsl-40 was proved to be sex-related, but sex-biased heterozygosity varied between populations for RAD-seq and validation, showing no evidence for sex chromosomes or single-locus models for C. gigas primary sex determination. Information obtained in our study provides novel insight into sex determination mechanism in C. gigas.