Genetic mating systems are expected to vary among and within populations in response to environmental and demographic factors. Despite the fact that mating system variation theoretically can have profound effects on important evolutionary processes such as sexual selection, extensive intraspecific surveys of geographical variation in mating systems are rare. We used microsatellite markers to characterize genetic mating systems of dusky pipefish, Syngnathus floridae, from five populations distributed from the mid-Atlantic Coast to the Western Gulf of Mexico. We also measured a number of environmental and demographic variables to examine correlations between the ecological setting and mating behaviour. Our results show that dusky pipefish are polygynandrous throughout their USA distribution, but they exhibit a wide range of quantitative variation in male mating behaviour. In addition, these five populations varied substantially with respect to environmental and demographic variables, and some of these were significantly correlated with aspects of the genetic mating system. While causal relationships cannot be firmly diagnosed from this type of comparative study, our results do identify several ecological factors, such as water temperature, adult sex ratio, and seagrass biomass, which should be considered in future experimental and comparative work. Overall, this study confirms the expectation that geographical variation in mating systems is widespread and shows that the dusky pipefish is an excellent model for continued research into the factors affecting mating systems in nature.