Although variation in male fertilization efficiency has been shown to have a genetic basis in several species, the genes responsible for the effect are generally unknown. Here, we show a strong association between the fertilization success of males and their phosphogluconate dehydrogenase (Pgdh) genotype in the bulb mite Rhizoglyphus robini. Males homozygous for the slow (S) allele fathered a significantly greater proportion of offspring when competing with males homozygous for the fast (F) allele. There was no evidence that female fecundity was influenced by their Pgdh genotype. The fecundity of FF females did not differ significantly from the fecundity of SS females but female fecundity was significantly influenced by the genotype of their mate. Females paired with SS males laid significantly fewer eggs than females paired with FF males. Altogether these data show a trade-off, with the male SS genotype associated with their higher fertilization efficiency but at the cost of a negative impact on the fecundity of females mating with them.