Distributions of flying-fox (Pteropus alecto and P. scapulatus) were examined in relation to use of habitat in the essentially natural landscape of northern Australia. There were differences between the species in terms of the vegetation used for roosting and foraging, which were related to the reproductive cycle and seasonal variation in temperature, rainfall and the availability of preferred foods. Important habitats of P. alecto varied seasonally and included floodplain, mangrove, monsoon rainforest, Melaleuca open-forest, and Eucalyptus miniata/E. tetrodonta open-forest and woodland. The minimum scale at which conservation of P. alecto should be attempted is in the order of 5000 km2, based on seasonal patterns of habitat use. The size of this area will make conservation via traditional reserves difficult and conservation of important habitats outside reserves will be needed. Habitats protected for the benefit of P. alecto will also benefit P. scapulatus but because P. scapulatus is more mobile, displays greater yearly variation in distribution and is less well understood than P. alecto, appropriate conservation actions are less certain.