As habitat disturbance and inbreeding increasingly stress natural populations, ecologists are in urgent need of simple estimators to measure their impact. It has been argued that developmental instability (DI) could be such a measure. Observed associations between DI and environmental or genetic stress, however, are largely inconsistent. We here test whether an interaction between habitat disturbance and inbreeding could, at least partly, explain these discordant patterns. We therefore studied individual estimates of fluctuating asymmetry (FA) and of inbreeding in three populations of the critically endangered Taita thrush that are differentially exposed to habitat disturbance following severe forest fragmentation. As predicted, the relationship between DI and inbreeding was pronounced under high levels of disturbance, but weak or nonexistent under less disturbed conditions. Examining this relationship with mean d2, an allelic distance estimator assumed to reflect ancestral inbreeding, did not reveal any significant trend, hence suggesting that inbreeding effects in the Taita thrush are fairly recent.