Loquat is originated from China and it has spread to Pakistan. It is achieving significant value in the country. Present research work is a part of the first ever study on Mucor rot infecting loquat in Pakistan. Prevalence of Mucor rot was 100% in all surveyed locations and disease incidence was recorded as 34%, 40%, 43%, 45%, 49%, 51%, 53% and 56% in Choa Saiden Shah, Kalar Kahar, Murree, Chattar, Tret, Khan pur, Wahcant and Taxila respectively. Morphological characters such as color, texture and spore formation confirmed Mucor fragilis as the causal organism of loquat rot. For authentic identification, polymerase chain reaction (PCR) assay was conducted and nucleotide sequences of rDNA region (ITS1, 5.8S and ITS2) of Pakistani isolates (KT312816 and KT312817) were compared with available nucleotide sequences of six phyto-pathogenic Mucor species reported from nine different countries. Both isolates were exhibiting 99.98% genetic homology with M. fragilis. Morpho-molecular identification and pathogenicity tests are reliable tools for the confirmation of Mucor rot infection loquat in Pakistan and this information will be helpful for proper management of this disease.