This work aimed to perform the molecular identification of fungi mango fruits, in addition to verifying the effect of the essential oils for microbial control. Pericarp segments containing injured and healthy areas of mango fruits were initially disinfested, and then incubated in PDA culture medium at 25 °C. From all isolated material, UDC03, UDC04, UDC09 and UDC12 were preselected, which presented homogeneous cultures. The UDC04 and UDC12 isolates were submitted to the sequencing of the ITS region for presenting mycelial growth both greater and morphologically distinct of fungi from Colletotrichum genus. When BLAST is used in species identification, it was observed that UDC04 and UDC12 belong to Botryosphaeria dothidea and Neofusicoccum parvum, respectively. Regarding the control of UDC04, it was observed that BDA culture medium containing 1.5 to 2% of lemongrass and eucalyptus oils resulted in complete inhibition. For UDC12, mycelial growth inhibition was detected with the use of 1% and 1.5% essential oils of eucalyptus and lemongrass, respectively. The chia essential oil was not effective for the isolates control. Finally, the results reveal the importance of molecular identification of these phytopathogens associated with the establishment of an alternative control of fruits due to problems of contamination with chemical products.