Madagascar is one of the world's biodiversity hotspots. The island's past and current rates of deforestation and habitat disturbance threaten its plethora of endemic biodiversity. On Madagascar, tavy (slash and burn agriculture), land conversion for rice cultivation, illegal hardwood logging and bushmeat hunting are the major contributors to habitat disturbance. Understanding species-specific responses to habitat disturbance across different habitat types is crucial when designing conservation strategies. We surveyed three nocturnal lemur species in four forest types of varying habitat disturbance on the Masoala Peninsula, northeastern Madagascar. We present here updated abundance and density estimates for the Endangered Avahi mooreorum and Lepilemur scottorum, and Microcebus sp. Distance sampling surveys were conducted on 11 transects, covering a total of 33km after repeated transect walks. We collected data on tree height, bole height, diameter at breast height, canopy cover and tree density using point-quarter sampling to characterise the four forest types (primary lowland, primary littoral, selectively logged and agricultural mosaic). Median encounter rates by forest type ranged from 1 to 1.5 individuals (ind.)/km (Microcebus sp.), 0-1 ind./km (A. mooreorum) and 0-1 ind./km (L. scottorum). Species density estimates were calculated at 232.31 ind./km2 (Microcebus sp.) and 121.21 ind./km2 (A. mooreorum), while no density estimate is provided for L. scottorum due to a small sample size. Microcebus sp. was most tolerant to habitat disturbance, exhibiting no significant effect of forest type on abundance. Its small body size, omnivorous diet and generalised locomotion appear to allow it to tolerate a variety of habitat disturbance. Both A. mooreorum and L. scottorum showed significant effects of forest type on their respective abundance. This study suggests that the specialist locomotion and diet of A. mooreorum and L. scottorum make them susceptible to the effects of increasing habitat disturbance.