Black pod disease (BPD) is one of the most destructive diseases affecting cacao worldwide and is caused by several species of Phytophthora. In Mexico, the etiology of this disease has historically been attributed mainly to Phytophthora capsici, whereas the presence of P. palmivora has only recently been confirmed. The objective of this study was to characterize Phytophthora strains causing BPD in cacao plantations in southern Mexico using an approach combining multilocus phylogeny, morphology, and physiological traits. A total of 79 isolates were obtained from symptomatic cacao pods collected in the states of Tabasco and Chiapas. The ypt1 sequence was used for preliminary species identification. Nineteen representative strains were subsequently analyzed using a multilocus approach including the ITS, β-tubulin, COI, ypt1, and HSP90 regions. Maximum likelihood phylogenetic analyses confirmed their placement within the lineages of P. palmivora (clade 4) and P. tropicalis (clade 2b). Both species exhibited optimal mycelial growth between 25 and 30 °C. Pathogenicity assays confirmed that strains of both species produced typical BPD symptoms. Molecular, morphological, and physiological analyses confirm the presence of P. palmivora in cacao plantations in southern Mexico and its coexistence with P. tropicalis, the predominant species associated with BPD in the evaluated locations.