Accurate information on the distribution, demography, and conservation status of endangered populations in threatened habitats are essential to provide the basis for conservation actions and management plans. Neglect of western Ecuador by biologists has resulted in a paucity of information of primate populations in the region. Capuchins (Cebus spp.) and howlers (Alouatta sp.) occur in the Tumbes-Chocó-Magdalena hotspot along the Pacific coast. We conducted the first primate survey in Pacoche Marine and Coastal Wildlife Refuge, one of the few protected areas in western Ecuador. Although the Pacoche refuge is protected, illegal activities inside the area include slash-and-burn agriculture and natural resource extraction. We surveyed 18 1-km transects within the protected area between April and July 2012 to evaluate the effects of anthropogenic disturbance and habitat characteristics on population densities of the Critically Endangered Ecuadorian white-fronted capuchin (Cebus aequatorialis) and the Vulnerable mantled howler (Alouatta palliata aequatorialis). We confirmed the presence of C. aequatorialis through direct observation on three occasions outside transects. The low detection rate of C. aequatorialis underscores the need for immediate conservation action for this species. Using a hierarchical distance sampling model, we predicted group size as a proxy of probability of detection and found that canopy cover explained group density of A. p. aequatorialis, following a half-normal Int J Primatol distribution. We estimated the mean density of A. p. aequatorialis as 12.4 ind./km 2 and the total population to be 621.5 individuals. The correlation between the density of A. p. aequatorialis and canopy cover underlines the need to preserve the remaining forest and its connectivity. Our results also highlight the importance of including vegetation structure in primate censuses.