Habitat loss and fragmentation would often induce delayed extinction, referred to as extinction debt. Understanding potential extinction debts would allow us to reduce future extinction risk by restoring habitats or implementing conservation actions. Although growing empirical evidence has predicted extinction debts in various ecosystems exposed to direct human disturbances, potential extinction debts in natural ecosystems with minimal direct human disturbance are little studied. Ongoing climate change may cause habitat loss and fragmentation, particularly in natural ecosystems vulnerable to environmental change, potentially leading to future local extinctions. Recent climate change would lead to extended growing season caused by earlier snowmelt in spring, resulting in expansion of shrubby species and thereby habitat loss and fragmentation of mountainous moorlands. We examined the potential extinction debts of species diversity and functional diversity (FD; trait variation or multivariate trait differences within a community) in subalpine moorland ecosystems subjected to few direct human disturbances. Plant species richness for all species and for moorland specialists were primarily explained by the past kernel density of focal moorlands (a proxy for spatial clustering of moorlands around them) but not the past area of the focal moorlands, suggesting potential extinction debt in subalpine moorland ecosystems. The higher kernel density of the focal moorland in the past indicates that it was originally surrounded by more neighborhood moorlands and/or had been locally highly fragmented. Patterns in current plant species richness have been shaped by the historical spatial configuration of moorlands, which have disappeared over time. In contrast, we found no significant relationships between the FD and historical and current landscape variables depicting each moorland. The prevalence of trait convergence might result in a less sensitive response of FD to habitat loss and fragmentation compared to that of species richness. Our finding has an important implication that climate change induced by human activities may threaten biodiversity in natural ecosystems through habitat loss and fragmentation.