We investigated the seasonal habitat selection of Mosquitofish to increase our understanding of the ecology and invasiveness of this species. Sampling was conducted during the reproductive and non-reproductive season of Mosquitofish in four habitat types: Alternanthera philoxeroides habitat, Typha angustifolia habitat, Paspalum distichum habitat, and no vegetation habitat. Mosquitofish catch per unit effort was significantly lower in Typha habitat than in the other three habitats during the reproductive season. T. angustifolia can exude allelopathic chemicals and have the potential to negatively influence western Mosquitofish abundance. In the non-reproductive season, catch per unit effort of Mosquitofish were significantly higher in Alternanthera habitat than in the other three habitats. These results suggest that mats of A. philoxeroides provided an insulating layer for Mosquitofish overwintering. Therefore, Mosquitofish could expand its range further north in China as A. philoxeroides spreads northward with climate change. We suggest that an effective way of controlling western Mosquitofish is through eradication of the invasive macrophyte (A. philoxeroides) stands while retaining and restoring more native emergent macrophyte (T. angustifolia) stands; this strategy could limit overwintering habitat for western Mosquitofish and may draw them into open water habitats where they can be more easily removed.