Transgenic mosquitoes are a potential tool for the control or eradication of insect-vectored diseases. For malaria, one possible strategy relies on the introduction of malaria-refractory transgenes into wild Anopheles mosquito populations that would limit their capacity to transmit the disease. The success of such an approach obviously depends on a variety of factors. By developing a model that integrates both population genetics and epidemiology, we explore how mosquito mating preferences and the cost and efficacy of refractoriness affects the long-term prevalence of malaria in humans subsequent to a single generation inundative release of male transgenic mosquitoes. As may be intuitively expected, mating discrimination by wild-type individuals against transgenic ones generally reduces the probability that transgenes become stably established at a high frequency in mosquito populations. We also show that in circumstances where transgenic individuals exhibit some degree of discrimination against wild-type individuals, this can favour the spread of refractory alleles and lead to a significant reduction in malaria prevalence in the human population (if the efficacy of a dominant refractory mechanism exceeds at least 75%). The existence of such a non-intuitive outcome highlights the practical value of increasing the understanding of Anopheles mating preferences in the wild as a means to harness them in the implementation of population replacement approaches. Potential strategies by which previously described mating preferences of Anopheles gambiae populations could be exploited to manipulate the mate choice of transgenic release stocks are discussed.