Severe tropical cyclones are a major cause of episodic mortality for Pacific Island flying foxes (large fruit bats). Many flying foxes starve after forests are stripped of food sources, and hunting by humans may also increase in the post-cyclone period. In December 2001, Cyclone Waka passed directly over the Vava'u Islands in the Kingdom of Tonga, western Polynesia. We visited the islands 6 mo later to survey the flying fox (Pteropus tonganus) population and assess availability of potential food items (fruit and flower) in primary, secondary and plantation forests. Less than 20% of the pre-cyclone bat population (surveyed in 1999–2001) remained 6 mo after the storm. The density of potential food trees in flower or fruit at this time was only 15% of pre-cyclone density, and the main species available were different in the two time periods. The highest density of potential food trees occurred in secondary forest (26 flowering or fruiting trees ha−1) and plantations (23 ha−1); primary forest offered the least food (18 ha−1). Since 65–70% of the land area has been converted to agricultural plantations, this vegetation type had the highest absolute number of food-bearing trees – almost seven times that of primary forest. Flowering coconuts (Cocos nucifera) were the most abundant food source overall and we suggest that this species may be important in sustaining flying foxes following severe storms.