Free glutamate is a characteristic amino acid with a fresh taste. A high free glutamate content can increase the flavour of clams and better meet consumer demands. GDH is involved in the production of glutamate from a-ketoglutarate and determines the speed and direction of reaction in the glutamate metabolic pathway. In this study, we cloned a full-length cDNA of MpGDH homologues in the clam Meretrix petechialis and further investigated the relationship among MpGDH gene polymorphisms, gene expression levels, enzyme activity and glutamate content traits. A significant positive correlation of MpGDH gene expression with free glutamate content was observed (r = 0.62, p < 0.05). The relationship of variation in MpGDH gene expression with its SNP genotype and SNP haplotype was assessed. Five SNPs were found to be significantly associated with MpGDH gene expression (p < 0.05), from which we constructed two main haplotypes due to linkage disequilibrium. The results showed that haplotype H2 may be an effective haplotype associated with high MpGDH gene expression and high free glutamate content. The genetic effect of different haplotypes was validated by different family materials, which showed that MpGDH gene expression level of the H1H2 heterozygous genotype were significantly higher than those of the homozygous genotype H1H1 (p < 0.05). In summary, our findings revealed the potential influence of the MpGDH polymorphism on the free glutamate content and provided molecular biological information for the selective breeding of good-quality traits of M. petechialis. •The full-length cDNA sequence of MpGDH has been identified from the clam Meretrix petechialis.•The expression of MpGDH gene was significantly positively correlated with the content of free glutamate.•A significant association between a haplotype and the expression level of MpGDH gene were identified.•The haplotype H2 may be an effective haplotype associated with high MpGDH gene expression and high free glutamate content.