With the accelerating urbanization, natural habitats were fragmented or obliterated. However, landscape change does not immediately lead to species loss, but often causes a time-delayed extinction of species, which is called the term “extinction debt”. Species with unique ecological demands or life-history attributes are more prone to bear future extinction debt than species with a broader niche. For example, annual Orchid species. Previous studies demonstrate that underlying extinction debt under various spatial scales is relatively under-researched. Also, species' spatial patterns can impact the magnitude of extinction debt. Therefore, the specific objectives of this study were (1) to find out whether endangered Orchids have extinction debts in urban ecosystems. Is the extinction debt in the Orchid species under different spatial scales still the same? (2) to investigate the relationship between environmental determinants (Habitat quality and Urban development factors) and the presence of plant species which prone to bear extinction debts. (3) to test whether the spatial distribution patterns (aggregation or dispersion) of Orchids in patches correlated with extinction debt appearance. Here, we explored extinction debts of Orchid species based on habitat loss and their spatial distribution in urban ecosystems by using 3 endangered Orchids from 109 patches in Kanto region-highly urbanized area.