The genus Lasiodiplodia includes numerous plant-pathogenic species whose delimitation is complicated by overlapping morphological traits and limited resolution of common genetic markers. Lasiodiplodia brasiliensis was described as a species closely related to L. theobromae; however, its taxonomic status remains controversial. In this study, we re-evaluated the species boundaries between L. theobromae and L. brasiliensis using an integrative approach that combined multilocus and genome-scale phylogenetic analyses with morphological comparisons. Multilocus phylogenetic analyses based on ITS, tef1-α, tub2, and rpb2 revealed an unresolved relationship between the two taxa. The L. theobromae clade had low bootstrap support, whereas the ancestral node connecting both species had high support. In contrast, genome-scale phylogenetic analysis using hundreds of single-copy orthologous genes strongly supported a single monophyletic clade encompassing isolates assigned to both L. theobromae and L. brasiliensis. Morphological analyses further revealed that conidial dimensions and other diagnostic characteristics largely overlapped between the two taxa, rendering them unreliable criteria for species separation. Considering the combined molecular and morphological evidence, our results support treating L. brasiliensis as a synonym of L. theobromae. Clarifying species boundaries within this group helps stabilize the taxonomy of Lasiodiplodia and provides a reliable foundation for accurate pathogen identification and disease management.