Mating causes considerable alterations in female physiology and behaviour, and immune gene expression, partly due to proteins transferred from males to females during copulation. The magnitude of these phenotypic changes could be driven by the genotypes of males and females, as well as their interaction. To test this, we carried out a series of genotype by genotype (G × G) experiments using Drosophila melanogaster populations from two distant geographical locations. We expected lines to have diverged in male reproductive traits and females to differ in their responses to these traits. We examined female physiological and behavioural post-mating responses to male mating traits, i.e. behaviour and ejaculate composition, in the short- to mid-term (48 hours) following mating. We then explored whether a sexually transferred molecule, sex peptide (SP), is the mechanism behind our observed female post-mating responses. Our results show that the genotypes of both sexes as well as the interaction between male and female genotype affect mating and post-mating reproductive traits. Immune gene expression of three candidate genes increased in response to mating, and was genotype-dependent but did not show a G × G signature. Males showed genotype-dependent SP expression in the seven days following eclosion, but female genotypes showed no differential sensitivity to the receipt of SP. The two genotypes demonstrated clear divergence in physiological traits in short- to mid-term responses to mating, but the longer-term consequences of these initial dynamics remain to be uncovered.