The annual timing of reproduction is a key life history trait with a large effect on fitness. Populations often vary in the timing and duration of reproduction to adapt to different seasonality of ecological and environmental variables between habitats. However, little is known about the molecular genetic mechanisms underlying interpopulation variation in reproductive seasonality. Here, we demonstrate that the three-spined stickleback (Gasterosteus aculeatus) is a good model for molecular genetic analysis of variations in reproductive seasonality. We first compiled data on reproductive seasons of diverse ecotypes, covering marine-anadromous, lake and stream ecotypes, of three-spined stickleback inhabiting a wide range of latitudes. Our analysis showed that both ecotype and latitude significantly contribute to variation in reproductive seasons. Stream ecotypes tend to start breeding earlier and end later than other ecotypes. Populations from lower latitudes tend to start breeding earlier than those from higher latitudes in all three ecotypes. Additionally, stream ecotypes tend to have extended breeding seasons at lower latitudes than at higher latitudes, leading to nearly year-round reproduction in the most southern stream populations. A review of recent progress in our understanding of the physiological mechanisms underlying seasonal reproduction in the three-spined stickleback indicates that photoperiod is an important external cue that stimulates and/or suppresses reproduction in this species. Taking advantage of genomic tools available for this species, the three-spined stickleback will be a good model to investigate what kinds of genes and mutations underlie variations in the physiological signalling pathways that regulate reproduction in response to photoperiod.