Puerto Rico’s forest cover decreased to less than 10% in the early 1900’s leaving few forest patches available for migrant and resident birds. In this process of deforestation karst hills and coastal wetlands have been some of the most severely modified forest types; however, we know little about their bird community dynamics and their relation with habitat variables. To address this issue we studied bird species composition and habitat characteristics in karst forest and two coastal forested wetlands (mangrove and Pterocarpus forest) in the Caribbean island of Puerto Rico. In each forest type, we conducted 10 point counts monthly for two years and characterized habitat variables. We performed a non-metric multidimensional scaling (NMS) ordination and a multi-response permutation procedure (MRPP) for each year to determine the similarity of bird species composition among monthly censuses and the relation between species composition and habitat variables. This ordination technique grouped censuses into three groups: karst forest, Pterocarpus and mangrove in the migratory period, and Pterocarpus and mangrove in the non-migratory period. The high tree species richness in the karst forest, and the presence of standing water in coastal wetlands were the most important habitat variables associated with the different bird communities. Our results demonstrate that the karst and coastal wetlands forests, even if they are small patches surrounded by a mixed matrix of pasture and urban settlements may be important habitat for both residents and migrants, and suggest that the protection and restoration of these habitats should be high management and conservation priorities.