Tovomita is a Neotropical clade of Clusiaceae that includes 52 species widely distributed throughout the Amazon, Atlantic, Antilles, and Chocoan/southern Mesoamerican rainforests. Species-level relationships within Tovomita remain largely unexplored, thus hindering our understanding of their biogeography and the evolution of key morphological characters in the genus. Here, we inferred a plastid genome phylogeny containing 18 Tovomita species using maximum likelihood and Bayesian inference approaches. Our results indicate that current infrageneric classification of Tovomita, which relies largely on leaf venation, does not reflect phylogenetic relationships. Instead, we identify carpel number as a more reliable morphological trait for infrageneric classification: clades within Tovomita tend to include species that possess either four or five (or more) carpels. Moreover, groups of species within Tovomita tend to exhibit a high degree of geographic endemicity corresponding to their clade affiliation: species within these clades are restricted to either Amazon or Atlantic forests. The well supported clade of Atlantic forest inhabitants we identify is sister to a clade of mostly Amazonian species that also includes Amazon and Atlantic forest disjunct species, which are more closely related to Amazonian than to other Atlantic forest species. These findings represent a first important step in elucidating morphological evolution and biogeography in this widespread genus of neotropical rainforest trees and shrubs.