Aim Exceptions to the quasi-ubiquitous latitudinal diversity gradient (LDG) have been poorly studied. A reverse LDG, when species richness (SR) increases away from the Equator, has been suggested for several taxa and entire biomes. The Neotropical seasonally dry tropical forests (SDTF) are a well-known example of a reverse LDG that could be caused by the climatic stability of Pleistocene Refugia and dispersion from distinct source areas. Here, we test these predictions under a spatial and phylogenetic framework. Location Neotropics. Taxon Woody plants. Methods We used a recent species-level seed plant phylogeny and the DRYFLOR dataset to evaluate the geographic patterns of phylogenetic diversity (PD) and structure of woody plant assemblages associated with the Neotropical SDTFs. We conducted spatial regressions to test the effect of climatic instability since the Last Glacial Maximum (LGM) on assemblages’ residual PD (controlling for SR) and null model analysis to evaluate their phylogenetic structure using the Net Relatedness Index. Results Phylogenetic diversity of the Neotropical SDTFs increased away from the Equator, likely driven by SR. This pattern was not related to climatic instability since the LGM. Phylogenetic structure of SDTF assemblages showed considerable spatial patterning, with significant phylogenetic clustering in the Mesoamerica and Caatinga regions. Main conclusion The reverse latitudinal SR gradient of the Neotropical SDTF assemblages is mirrored by their PD. Phylogenetic history seems to have influenced such patterns differently across the Neotropics with no relationship to climatic stability since the LGM, where particular SDTF nuclei previously suggested as Pleistocene refugia served as cradles and source areas for the current diversity pattern of the biome.