Environmental and past land use controls on tree species assemblages on the Commonwealth of Puerto Rico and the U.S. Virgin Islands were characterized to determine whether biophysical factors or land-use history has been more important in determining the species composition of secondary tropical forests after large-scale forest clearing for agriculture, widespread species introduction, and landscape-scale forest fragmentation. Post de-forestation, secondary forest assemblages are comprehensively described, both as broad general assemblages and island-specific variations by calculating species importance values from forest inventory data. Hierarchical clustering and indicator species analysis defined species assemblages, and then correlations between species assemblages and environmental variables were explored with non-metric multidimensional scaling, analysis of variance and X2 testing. These assemblages are arrayed along environmental gradients of decreasing spring moisture stress, decreasing maximum temperatures, and increasing minimum temperatures. Land-use history is not as important to determining variation in species composition across climatic zones, although several species assemblages are associated with certain geology types or land-use histories. Naturalized tree species are prominent in these secondary forests and contribute to the formation of some novel assemblages, but native late and early successional species also colonize former agricultural land, all influenced by the degree of disturbance. We conclude that environmental factors have an overarching effect on forest species composition across the broader range of climatic, geologic and topographic conditions and larger geographic scales, while land-use history influences subtropical secondary forest species assemblages with a specific climatic zone or set of relatively narrow environmental conditions.