The black pod disease of cocoa in Ghana caused by Phytophthora palmivora and P. megakarya is traditionally managed with fungicides. Because of challenges associated with fungicide use, biological control options, if available, are worth trying. A fungus with proven usefulness in suppressing P. palmivora and P. megakarya in dual plate cultures and cocoa pods has partly been identified as an Aspergillus (designated AI_1). However, its exact identity has been unknown, requiring specific identification by comparing it with known Aspergillus flavus strains (designated AI_2, AI_3, AI_4, and AI_5). It was retested against P. palmivora to confirm the potency of AI_1. The putative A. flavus isolates were also tested for the first time against P. palmivora. Morphological features were determined on carrot agar (CA), potato dextrose agar (PDA), and malt extract agar (MEA). Genomic DNAs from the Aspergillus isolates were subjected to the ITS region and β-tubulin gene sequencing. All the Aspergillus isolates inhibited P. palmivora in assay plates by levels ranging from 89.33 to 95.33% (Experiment 1) and 46.67 to 60.33% (Experiment 2). Generally, the AI_1 produced culture features similar to those of the putative Aspergillus flavus isolates. ITS region sequence analysis grouped all isolates as A. flavus and beta-tubulin also grouped AI_1, AI_2, AI_3, and AI_4 as A. flavus but differentiated AI_5 as A. flavus var. parvisclerotigenus. AI_3 recorded the highest inhibition zone and prevented black pod development of inoculated pods as well. The previously unknown Aspergillus isolates AI_1 is now conclusively identified as A. flavus.