Much attention has been directed to understanding species richness patterns, but adding an evolutionary perspective allows us to also consider the historical processes determining current diversity patterns. We analyzed phylogenetic patterns of fern species assemblages in 868 plots along a wide range of elevational (0-4000 m) and latitudinal (0°-23°N) gradients in the Neotropics to allow a deeper understanding of evolutionary processes underlying current patterns of diversity and community assembly. Overall, we found that phylogenetic mean pairwise distance (sMPD) and mean nearest taxon distance (sMNTD) decreased with increasing latitude and elevation, but that these geographical factors per se were weak explanatory variables. Incorporating environmental variables strongly enhanced the power of the predictive model, indicating that fern assemblages are phylogenetically more diverse under wet and warm to cool conditions at low latitudes and elevations. Further, whereas epiphytic fern assemblages were strongly influenced by climatic factors, this was not the case for terrestrial ones, suggesting that edaphic conditions and vegetation structure may have a stronger influence on the evolution and diversification of terrestrial ferns. We conclude that fern assemblages are strongly influenced by phylogenetic niche conservatism and environmental filtering. This has also been found for angiosperms, but the direction of the environment-phylogenetic relationship is often opposed in the two groups, suggesting that the older age of many fern lineages includes historical signals that are not evident in the more recent angiosperm radiation.