Recent theory suggests that habitat preference divergence, as opposed to species recognition divergence, is a relatively likely outcome of genetically incompatible hybridization (i.e. reinforcement by habitat isolation). Habitat preference is typically assumed as a sexually shared trait in speciation models, but the fitness consequences of habitat preference can be sex specific. In addition, complete reproductive isolation is not necessarily an adaptive optimum. Here I theoretically examine the evolutionary dynamics of sex-specific habitat preferences during the secondary contact with hybridization. When the two species can discriminate against each other to some extent, males and females show different contributions to the eventual establishment of habitat isolation. Species discrimination is typically unfavorable for habitat isolation, leading to the extinction of either species. Adaptively maintained partial habitat segregation in not found in either sex, and males and females evolve similar habitat preferences. Habitat divergence is more likely when genetic basis of habitat preference is sexually shared than when habitat preference is sex-specific. These findings help us understand the evolutionary dynamics of reinforcement by habitat isolation.