Cities are expanding rapidly worldwide. Modern cities are expected to carry heavy extinction debts owing to their recent and drastic fragmentation histories. Therefore, detecting extinction debt and identifying species threatened by it in recently created cities are necessary to prevent future biodiversity losses. Here, we studied the relationship between the life-history traits of butterfly species and the extent of their extinction debts using two different methodological approaches in Tokyo, central Japan. First, we compared the effects of current and past landscape parameters on current species richness using generalized linear models. Second, we predicted species richness in unstable (i.e. high loss) habitats using a model developed for stable (i.e. low loss) habitats. The difference between predicted and observed species richness was used to estimate the extinction debt (the number of species expected to go extinct). We classified butterfly species as seasonal specialists or generalists and as habitat specialists or generalists based on their life-history traits. With both methods, we found significant extinction debts only for specialist species. Mapping the potential extinction debts within our study area indicated that currently large patches had relatively low extinction debts, whereas small patches often had high extinction debts. These results suggested that improving patch area, connectivity and especially quality, would have more significant impacts in small patches than in large ones. Extinction debt is an important concept for setting conservation priorities in highly fragmented landscapes, especially in urban areas.