Loquat is a fruit of subtropical areas grown in various countries of the world. Owing to its high nutritional value, it is prone to various postharvest fungal diseases deteriorating fruit quality and heavy economic losses. The study aimed to identify Rhizopus stolonifer causing soft rot of loquat fruit. During a survey in the local fruit markets of districts Rawalpindi, Attock, Chakwal and capital territory Islamabad during the months of April and May 2017, symptomatic samples of rotted loquat fruits were collected for identification of the causal organism. The pathogen was isolated on potato dextrose agar (PDA), purified on Czapek dox agar (CDA) and was confirmed as Rhizopus stolonifer based on morphological characteristics including mycelial growth pattern, size, color and shape of sporangia and sporangiophores. Sporangiophores were globose, ellipsoidal and angular in shape with erected hyphae. The size of sporangia ranged from 120-190 µm. The diameter of sporangiophores ranged from 14~18 µm whereas length varied from 460~2800 µm. The sporangiospores were ranged from 12~14 × 245 µm in size while the size of columella was up to 120 µm. The results of the morphological identifications were further confirmed by sequence analysis of the internal transcribed spacer region (ITS) using a set of universal primers ITS1 and ITS4. Koch’s postulates were fulfilled by re-isolation of the pathogen from artificially inoculated loquat fruits. To the best of our knowledge, this is the first report of Rhizopus stolonifer causing postharvest soft rot of loquat fruit in Pakistan. The results of the present investigations will be helpful in devising control strategies to manage this disease.