In Pakistan, loquat (Eriobotrya japonica) is becoming a major fruit crop for local and export markets but its yield is continuously declining. The aims of the current study were to determine the geographical distribution, incidence and morpho-molecular identification of major fungal pathogens associated with loquat in Punjab, Pakistan. For this purpose, a total number of 34 loquat orchards were surveyed during summer and winter 2014 and summer and winter 2015 in loquat growing areas of Punjab. A total number of 2720 samples (fruit, leaves and twigs) were collected from Taxila, Wah Cantt, Khanpur, Tret, Chatar, Murree, Kalar Kahar and Choa Saiden Shah. Alternaria leaf spots and fruit rot, twig dieback, anthracnose, Curvularia leaf spot and fruit rot and Fusarium fruit rot were recorded in all locations. Fungal diseases were found in all orchards and average incidence was recorded as 25.55 percent and 27.6 percent of tree in two consecutive years. The environmental conditions for the development of fungal diseases were more favorable in summer as compared to winter and due to this, the disease incidences recorded higher in summer. During the second year, increases in fungal diseases incidence were recorded in Taxila (6 percent), Wah Cantt (5.5 percent), Khanpur (1.7 percent), Tret (1.65 percent), Choa Saiden Shah (1 percent), Chatar (0.85 percent) and Murree (0.65 percent), due to dispersal of infected loquat debris in loquat orchards. A reduction in disease incidence was observed in Kalar Kahar (1 percent) due to the proper sanitation measures. Alternaria alternata, A. mali, Curvularia lunata, C. geniculata, Colletotrichum gloeosporioides, C. capsici, Fusarium solani and F. equiseti were isolated from the infected loquat fruit and leaves while only Lasiodiplodia theobromae was observed to cause twig dieback of xvii loquat. A total number of 843 isolates were confirmed through morphological characterizations. Alternaria sp. was exhibiting the maximum (168) isolates followed by L. theobromae (146), Colletotrichum capsici (140), Fusarium sp. (136), C. gloeosporioides (131) and Curvularia sp. (122) and Alternaria leaf spot and fruit rot was prominent in Tret (26.54 percent), Khanpur (26.19 percent), Taxila (25.76 percent) and Wah Cantt (19.23 percent) while maximum incidence of Curvularia leaf spot and fruit rot, Fusarium fruit rot, twig dieback and anthracnose (C. capsici) was recorded in Chatar (20.59 percent), Murree (20.58 percent), Choa Saiden Shah (20 percent) and Kalar Kahar (17.86 percent) respectively. The pathogenic abilities of each isolate were checked on healthy loquat plants, detached leaves and fruit. The internal transcribed spacer regions (ITS1, 5.8S and ITS2) of 44 highly virulent fungal isolates was amplified through PCR assay and sequencing analysis of ITS regions exhibited 99 to 100 percent genetic homology with previously reported isolates. Five multi-genes sequence analysis viz ITS, translocation elongation factor 1-α (EF), beta-tubulin (BT), actin (ACT) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) confirmed these pathogens at species level. The morphological characterization and multigene sequence analysis confirmed Lasiodiplodia theobromae, Curvularia lunata, C. geniculata, Colletotrichum gloeosporioides, C. capsici, Alternaria mali, A. Alternata, Fusarium solani and F. equiseti. The geographical distributions, incidences and morpho-molecular identification of major fungal pathogens is providing the guidelines for new researcher working on disastrous pathogens of loquat in Punjab Pakistan and this information will act as a remedy for development strategies of proper management of these destructive fungal pathogens.