In Brazil, the Annonaceae species Annona muricata , A. squamosa , A. cherimola and atemoya (a hybrid of A. cherimola and A. squamosa ) are cultivated in several regions, and produce fruits that are highly appreciated by consumers and are of great economic importance. Among the several diseases that can affect these crops, dieback is one of the most important, causing damage and, in the most severe cases, death of the plants. Due to the lack of suitable diagnostic studies up to now, this work aimed to identify the Botryosphaeriaceae species that cause dieback on Annonaceae in Brazil. Based on combined phylogenetic analyses of ITS, TEF‐1α , TUB2 and RPB2 , eight species of Botryosphaeriaceae were identified, namely Lasiodiplodia brasiliense , L . crassispora , L . hormozganensis , L . iraniensis , L . pseudotheobromae , L. subglobosa , L . theobromae and Pseudofusicoccum stromaticum . All species found in this study were pathogenic and caused symptoms of necrosis in stems and dieback. Thus, this study confirms species of Botryosphaeriaceae as causal agents of dieback on Annonaceae in Brazil.