The health status of treated banana bunches in three boxes was assessed 48 hours and 21 days of storage for two consecutive years. The colonies grown on bananas after the conservation periods were isolated, identified and counted by fungal genus. Similarly, developed symptoms on bananas have been described. The prevalence of each observed postharvest disease was evaluated. The prevalence of crown rot ranged from 4 to 98% while the necrosis of the epicarp and the decay of the distal end ranged respectively from 0 to 70 and 0 to 61%. A pathogenicity test of fungi associated with the most prevalent disease was performed. Molecular identification of those responsible fungi of the most prevalent disease was done and phylogeny of these isolates was established. White mould was observed on the surface of banana end fingers after 48 hours without noticeable symptoms. However necrosis of the epicarp and crown rots and the distal end of bananas were observed after 21 days of conservation. Banana crown rot was the most prevalent postharvest disease. The pathogenicity test and molecular analysis showed that Phellinus noxius and Botryodiplodia theobromae were identified as the causative agents of banana crown rot disease in Côte d’Ivoire.