The American crocodile is widely distributed in coastal and lowland wetlands in the northern Neotropics. As a result of commercial skin hunting in the 20th century, populations were greatly diminished, but in many areas have initiated a period of recovery since hunting and trade controls were enacted in the 1980s and 1990s. While a great deal of attention has been devoted to regulated commercial use as a management strategy for recovering crocodilian populations, these approaches are limited in their efficacy to deal with issues of habitat loss and fragmentation. Because habitat limitations are expected to be the most critical issue for crocodile conservation in the 21st century, there is an unfulfilled need for alternative strategies that prioritize habitat conservation. Here, we present results of an international effort to identify and prioritize the most critical habitats for this wide ranging species. We quantified information of a group of American crocodile experts and classified 69 areas in eight distinct crocodile bioregions as Crocodile Conservation Units (CCU), the most important areas for the conservation of this species. The relative importance of the CCUs in each bioregion was quantified using an algorithm that weighted factors that the experts considered to be most important for the long term conservation of viable populations of crocodiles. This effort is the initial step in the development of a regional conservation plan for the American crocodile. We identified two bioregions in particular where the creation of protected areas should be given a high priority, the Dry Pacific South America (northern Peru and southern Ecuador) and the Northwest and Central Pacific Mexico.