The Mosquitia ecosystem of Honduras occupies the fulcrum between the American continents and as such constitutes a critical region for understanding past patterns of socio-political development and interaction. Heavy vegetation, rugged topography, and remoteness have limited scientific investigation. This paper presents prehistoric patterns of settlement and landuse for a critical valley within the Mosquitia derived from airborne LiDAR scanning and field investigation. We show that (i) though today the valley is a wilderness it was densely inhabited in the past; (ii) that this population was organized into a three-tiered system composed of 19 settlements dominated by a city; and, (iii) that this occupation was embedded within a human engineered landscape. We also add to a growing body of literature that demonstrates the utility of LiDAR as means for rapid cultural assessments in undocumented regions for analysis and conservation. Our ultimate hope is for our work to promote protections to safeguard the unique and critically endangered Mosquitia ecosystem and other similar areas in need of preservation.