Urban areas are highly dynamic landscapes and urbanization patterns are spatially complex. For effective wildlife management in urban landscapes, it is essential to consider the complex history of urbanization and its timedelayed effects on species distribution. We examined whether the history of local land use affects the time-delayed response of Japanese hares (Lepus brachyurus) to landscape change in an urban ecosystem by hierarchically reducing the factors affecting differences in the response. We evaluated the occurrence of hares in 62 forest patches along an urban gradient in the Tama Hills area, Japan. Using sites where the surrounding landscape remained relatively stable, we calculated the habitat threshold of hare occurrence based on the surrounding forest area. We extracted sites that used to be suitable for hare occurrence in the past but later on surpassed the identified habitat threshold (i.e., ‘regressive sites’) and analyzed the landscape factors explaining the extinction debt of hares. Finally, we mapped potential extinction debt throughout the study region. We detected possible extinction debt in 4 regressive sites. We also found that forest patch size and the number of surrounding forest patches were related to hare occurrence. Based on this prediction, several other sites with potential extinction debt were identified in the study region. We found that the delayed response of the Japanese hares is likely caused by differences in forest fragmentation processes at each site. Our hierarchical approach could be an effective methodology for detecting and explaining the cause of extinction debt at the local scale and would contribute to the management of urban land for wildlife conservation.