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Forty-six percent of tropical raptors are threatened by habitat loss and fragmentation. Tropical raptors are generally rare species. The scarce information on distribution patterns of rare species makes it difficult to establish reliable conservation plans. We used ecological niche modelling to obtain good predictions of occurrence of two case species, the rare and endemic Gundlach’s and Cuban Black-hawks in Cuba, based on presence-only data. We used records from an intensive survey undertaken in natural and modified environments. Data were integrated with environmental variables using Maxent to predict species distributions. Subsequently, we overlaid the resulting predicted distributions, the land use map and the protected areas layers to establish potential suitable habitat for these endemics and to determine if a better design of protected areas than the existing one can be proposed using both hawks’ distribution in the design. Gundlach’s Hawk distribution was fragmented, depending on forest distribution. Cuban Black-Hawk distribution was narrow, near the coastline. Forests and mangrove represent 57% and 45% of Gundlach’s Hawk and Cuban Black-Hawk model predictions, respectively. 71% of the total forest area was represented in the distribution of Gundlach’s Hawk. Mangrove area overlaps 45% of the Cuban Black-Hawk distribution. Six protected areas preserved 50% and 92% of their distributions, respectively. With few presence-only data of rare species, Maxent models were statistically and ecologically significant and reliable to develop distribution maps with high predictive power. Our results highlight the importance of natural habitats for conservation efforts of these endemic species. A good conservation program should include the protection of suitable nesting areas and expand the protected areas network containing suitable habitats for both species in forest and coastal areas. We propose the use of predictive modelling tools to strengthen conservation actions not only for rare raptors but for the 238 endemic and threatened birds of the Neotropics with scarce data, small population sizes, restricted distributions and often specialist habits.