Cacao (Theobroma cacoa L.) is an important tropical fruit tree used in chocolate production. Among the biotic problems interfering with fruit production, phytopathogenic fungi stand out. During a visit to cocoa production areas in the municipality of Medicilândia, Pará, Brazil (Amazon region), we observed cocoa fruits with dark lesions and greyish‐white cottony mycelia growth. In order to determine the aetiological agent's identity, we extracted DNA and amplified part of the TEF‐1α and RBP2 genes and compared them with sequences in GenBank using the BLASTn tool. Based on molecular results and phylogenetic analysis, the isolates were identified as Calonectria hawksworthii. Inoculations in cacao fruits showed symptoms after 6 days and were similar to those collected in the field, confirming the postulates. This study is the first report of Ca. hawksworthii causing cocoa bean rot worldwide.