Knowledge shortfalls remain a major barrier to understanding global biodiversity, especially in tropical hotspots such as the Brazilian Cerrado. Among these, the Darwinian shortfall—the lack of molecular and phylogenetic data—limits evolutionary and ecological inference and hampers conservation planning. The Tocantins-Araguaia Basin, a highly diverse region within the Cerrado, harbors numerous species of Fabaceae, one of the most diverse and ecologically relevant angiosperm families. However, the extent of molecular data coverage for these taxa remains poorly characterized. We compiled a list of Fabaceae species occurring in the Tocantins-Araguaia Basin using GBIF, SiBBr, speciesLink, and BIEN, filtered through Reflora nomenclature. Molecular data availability was assessed from BOLD Systems and NCBI, considering sequences, annotated genes, and genome assemblies. Phylogenetic representation was mapped onto the Legume Phylogeny Working Group (2017) tree, with species insertions performed in R using ape and visualized with ggtree. A total of 1,423 valid Fabaceae species were identified. Molecular coverage is uneven: the most common markers are ITS, ITS2, matK, rbcL, and rbcLa, but most species are represented by only one or none. Subfamilies such as Papilionoideae are relatively well covered, while Detarioideae and Dialioideae show significant data gaps. NCBI searches revealed a strong asymmetry, with few species having extensive nucleotide data or annotated genes, and complete genomes are extremely rare. These findings demonstrate that Darwinian shortfalls are not randomly distributed but phylogenetically structured, with data concentrated in a few economically important clades. This bias reduces the representativeness of phylogenies and limits conservation prioritization based on evolutionary distinctiveness. By identifying patterns of molecular data scarcity in Fabaceae of the Tocantins-Araguaia Basin, this study provides a framework for guiding future sequencing efforts and conservation strategies. Expanding molecular coverage will be crucial to strengthen biodiversity assessments in the Cerrado.