We conducted nocturnal surveys in the insular and coastal areas of Coiba National Park (CNP) and its mainland buffer zone in Panama (Chiriquí conservation site) from 2009–2012 to determine the conservation status of Crocodylus acutus. In 99 nights, we surveyed 147.2 km and captured 185 animals during nocturnal transects inspection with headlamps. Overall, sex ratio was 1.00:1.01 female/male with significant differences by size/age class and year. Females were slightly larger in total length than males (115.1 ± 56.9 cm-females, 105.4 ± 71.8 cm-males). The encounter rate was calculated based on number of animals captured per km of surveyed transect. The C. acutus encounter rate per year was 1.8 ind/km (60 ind/33.5 km/12 places visited) in 2009, 1.0 ind/km (90 ind/87.4 km/18 places visited) in 2010, and 1.3 ind/km (35 ind/26.3 km/8 places visited) in 2012. Based on our spatial analysis, the animals showed a dispersed pattern in most sites on CNP. Captured C. acutus were found in 581.1 km2 total area within 78% natural habitat, including mangroves and beaches, and 22% disturbed habitat on both the mainland and the islands. In addition, the spatial analysis showed reduction in natural land cover; crocodile habitat showed limited conversion to agricultural land use; and we found correlation between crocodile population size and protected areas. The differences between mainland and island populations regarding ecology suggest that a long-term monitoring program for American Crocodiles is necessary to distinguish between natural fluctuations and anthropogenic changes on population dynamics and conservation status.