Inter-sexual segregation between habitats or between sites within a habitat is very widespread in sexually dimorphic ungulates. As an explanation, it has been suggested that males, because of their larger forage requirements, are driven from preferred, high quality forage habitats into marginal habitats of lower forage quality but higher forage biomass by female competition (‘indirect competition hypothesis’). However, this hypothesis has hardly been tested. In the present study, we tested the indirect competition hypothesis for site segregation of red deer on the Isle of Rum, Scotland, within two vegetation communities: short Agrostis/Festuca grassland and Calluna heath. We predicted that: (1) males should choose sites within each vegetation community that are of higher forage biomass but lower forage quality, than sites selected by females; (2) the degree of inter-sexual site segregation should be highest within the vegetation community in which indirect competition was most intense. We found that the sexes were significantly segregated between sites within both vegetation communities, but males did not use sites of lower forage quality or of higher forage biomass than did females. Moreover, degree of site segregation was not significantly higher in the vegetation community in which competition was more intense (i.e. short Agrostis/Festuca grassland). We conclude that the indirect competition hypothesis cannot explain site segregation in red deer on the Isle of Rum.