Crown rot is a postharvest disease with a great negative impact on banana fruit quality. The infections occur at harvest, but the symptoms appear after overseas transportation. Different fungal pathogens are involved in crown rot, varying according to farming area. In this study we focused on etiology of organic banana crown rot in the Dominican Republic, which is one of the leading exporters of organic bananas. Bananas from five organic farms and their corresponding packing stations located in the Valverde province were studied. Over a period of three years, 558 banana hands were collected and a total of 5000 fungal colonies were obtained from the crown tissues and 518 representative colonies were purified, characterized and identified using morphological and molecular methods. Fungi were found in all samples from field and from packing house and were distributed in 11 genera. The fungal community was dominated by Fusarium, the most frequent genus (55%) found in more than 80% of all samples. The genus was represented by nine species; Fusarium incarnatum 53%, the most frequent, followed by Fusarium verticillioides 12%, Fusarium sacchari 12%, Fusarium proliferatum 7%, and Fusarium solani 6%. The five least frequent species were Colletotrichum musae, 7% overall frequency and found in 13% of all samples; Lasiodiplodia theobromae and Lasiodiplodia pseudotheobromae, 4% and 1% overall frequency, respectively, both species found in 7% of all samples; Nigrospora sp. 11% overall frequency, Alternaria spp. 6% overall frequency, followed by Phoma spp., Pestalotiopsis sp., Curvularia spp., Microdochium sp. and some other species, known to be saprophytes, with frequency lower than 2%. The etiological agents of crown rot disease can be ranked based on their presence and pathogenicity as follows: Fusarium incarnatum, Colletotrichum musae, Fusarium verticillioides, Fusarium sacchari, and Lasiodiplodia theobromae.