Differences among populations in the intensity of sexual selection resulting from distinct genetic mating systems can lead to divergent morphological evolution and speciation. However, little is known about how genetic mating systems vary between populations and what factors may contribute to this variation. In this study, we compare the genetic mating systems of two geographically distinct populations of the dusky pipefish (Syngnathus floridae), a species characterized by polygynandry and male pregnancy, from the Atlantic Coast of Virginia and the Gulf Coast of Florida. Our results revealed significant interpopulation variation in mating and reproductive success. Estimates of the opportunity for selection (I), the opportunity for sexual selection (Is) and the Bateman gradient (βss) were higher among males in the Florida population than in the Virginia population, suggesting that sexual selection on males is stronger in the Florida population. The Virginia population is larger and denser than the Florida population, suggesting that population demographics may be one of many causal factors shaping interpopulational mating patterns. This study also provides evidence that the adult sex ratio, operational sex ratio, population density and genetic mating system of S. floridae may be temporally stable over timescales of a month in the Florida population. Overall, our results show that this species is a good model for the study of mating system variation in nature and that Bateman's principles may be a useful technique for the quantitative comparison of mating systems between populations.