Throughout the tropics, pristine forests disappear at an alarming pace. This presents a severe threat to forest-dependent species. Especially dispersal-limited understory birds are affected by forest loss. We here explored the effects of habitat fragmentation on the genetic structure and the morphology of the Ecuadorian Tapaculo (Scytalopus robbinsi). This bird occurs only in a small range in the premontane cloud forests of southwestern Ecuador. The global population size is declining rapidly due to habitat loss and is currently estimated at only 3000 mature individuals. We caught a total of 28 Ecuadorian Tapaculos in forests of varying size in an area of about 40 km². From each bird, we took morphological measurements and a blood sample. This was used to develop a set of 10 species-specific microsatellite primers for genetic analysis and we found that the Ecuadorian Tapaculos display high levels of genetic diversity. Additionally, we identified dispersal corridors for the species across the landscape using a least-cost path analysis. Notably, we found that wing shape is related to forest size. Individuals in smaller fragments show adaptations of the wing morphology to enhanced mobility and better flight capacity. Our results suggest that the Ecuadorian Tapaculo may rapidly adapt its morphology to the level of habitat fragmentation. This potential can possibly mitigate the risk of local extinctions of the species due to human-caused forest loss and fragmentation.