A feature of many endangered species management plans, is the provision or protection of habitat. However, defining exactly what constitutes habitat can be difficult. This is made more complicated when habitat preferences differ within a species such as between males and females. Using a combination of field surveys and sex identification through fecal DNA, we investigated gender differences in habitat use in wild giant pandas through ecological niche factor analysis modelling. Our results indicated that both males and females tended to prefer areas at high altitudes and with high forest cover. However, significant sexual differences in habitat selection were also observed. Furthermore, habitat preferences of females are more restrictive than those of males, and females have a stronger association with high altitude conifer forest, mixed forest, historically clear-felled forest and >10 to ≤20° slopes. The more restricted habitat preferences of females could be explained by their need for dens for birthing and dense bamboo cover for concealing the young. Therefore, effective conservation and management strategies should consider these differences in habitat selection of females and males.