Sperm-dependent asexual species must coexist with a sexual species (i.e. a sperm source) to reproduce. The maintenance of this coexistence, and hence the persistence of sperm-dependent asexual species, may depend on ecological niche separation or preference by males for conspecific (i.e. sexual) mates. We first modified an analytical model to consider both of these mechanisms acting simultaneously on the coexistence of the two species. Our model indicates that a small amount of niche separation between parental species and hybrids can facilitate coexistence by weakening the requirement for male mate preference. We also estimated niche separation empirically in the Chrosomus (formerly Phoxinus) sexual-asexual system based on diet overlap between sperm-dependent asexuals and their two sexual host species. Diet overlap between the sexual species was not significant in either lake, whereas the sperm-dependent asexual had an intermediate niche that overlapped significantly, but somewhat asymmetrically, with both sexual species. These empirical results were then used to parameterize our analytical model to predict the minimum strength of male mate preference required to maintain coexistence in each lake. Some male mate preference is likely required to maintain coexistence in the Chrosomus system, but the minimum required preference depends on the severity of density dependence. Future empirical work on understanding coexistence in sperm-dependent asexual systems would benefit from taking both niche separation and mate choice into account, and from simultaneous empirical estimates of male mate choice, niche separation, and density dependence.