Several centers of endemism have been proposed for Melastomataceae, particularly in Amazonia and Atlantic Forest. Despite the high degree of human-caused degradation in the last 500 years, the Atlantic Forest still presents some of the largest levels of diversity and endemism across all angiosperms. With several recently described species in the last decade, the knowledge on Bertolonia’s distribution and morphological characterization has changed, with most new species found in northern Atlantic Forest and with different flower color patterns than the species from southern Atlantic Forest. We first tested the monophyly of the genus sampling over 85% of its species to generate a reliable phylogenetic hypothesis. Afterwards, we used Bertolonia as a model group to study distribution patterns and morphological evolution of lineages in the Atlantic Forest. Bertolonia is particularly interesting to address such questions because it is endemic to this domain, with species distributed either in the southern, central or northern portions of the Atlantic Forest. The second step of our work aimed to respond (1) Do closely related species endemic to Atlantic Forest tend to have similar distributions and share similar morphological traits? and (2) Are floral traits more conserved within clades than vegetative characters? We hypothesize that both (1) and (2) are true due to the low dispersal ability and consequent microendemic distribution of most species in the genus. Our results confirm the veracity of the proposed hypotheses. Three major groups were recovered in our analysis: marmorata, formosa and nymphaeifolia clades. Most species that occur in northern Atlantic Forest were recovered in the marmorata clade. Most species distributed in central Atlantic Forest were recovered in the formosa clade, and the ones from the southern Atlantic Forest in the nymphaeifolia clade. A similar pattern was recovered with reproductive characters reconstructed across the phylogeny. Generally, species with pink petals and cream-colored anthers with an extrorse pore occur in northern Atlantic Forest, and species with white petals and yellow anthers with an introrse or apical pore tend to occur in southern Atlantic Forest. Some vegetative characters also have evolutionary congruence and are restricted to one or few lineages, while other characters, such as the texture of the leaf blade surface, have a strong taxonomic value and are useful to identify species, but are not homologous. Our analysis also indicates that the division between southern and northern Atlantic Forest could also be related to ancient events, not only linked with recent phylogeographic patterns. Moreover, we suggest that the orientation of the anther pore in Bertolonia could be related with diversity of species and stability of its populations. In summary, we corroborate, based on the evolutionary history of Bertolonia, that closely related species endemic to Atlantic Forest tend to have similar distributions and share similar morphological floral traits.