Sapota (Manikara zapota) belongs to family Sapotaceae. This species has various properties in the traditional system of Indian medicine. In current study Kalipati variety of Sapota fruit is used. Sapota fruit is a rich source of sugar and hence it attracts number of fungal species. Two fungal species viz Aspergillus minisclerotigenes and lasiodiplodia theobromae were identified from infected fruits. In present study identification is based on microscopic and morphological characters Potato dextrose Agar, granulated medium is used for isolation of fungi and Rose bangal medium is used for pure culture. For molecular identification DNA sequencing reaction of PCR amplicon was carried out with ITS1 primer using BDT V 3.1 cycle sequencing kit on ABI 3730x1 Genetic Analyzer.