Mango (Mangifera indica), which is rich in nutritive value is affected by many biological factors including diseases. Postharvest diseases viz., anthracnose caused by Colletotrichum gloeosporioides and stem end rot caused by Lasiodiplodia theobromae are of economic importance due to loss in quality and quantity after harvesting. The pathogens C. gloeosporioides and L. theobromae were isolated from five mango varieties collected from fruit markets and farmers’ field of major mango growing districts of Tamil Nadu. The mycelial, colony and conidial characters were identified morphologically. Molecular characterization was carried through polymerase chain reaction using universal primers ITS1 and ITS4. The sequencing was done and the sequences were deposited in Genbank. From phylogenetic analysis Colletotrichum gloeosporioides showed maximum identity of 100% and Lasiodiplodia theobromae showed maximum identity of 88%. The present study confirmed that pathogen associated with anthracnose and stem end rot was Colletotrichum gloeosporioides and Lasiodiplodia theobromae respectively.