Loquat (Eriobotrya japonica Lindl.) is an important but ignored fruit crop of Pakistan for which no research work has ever been reported previously inside the country. There is no standard or identified loquat cultivar available to the growers for cultivation in the loquat growing pockets of Pakistan. Generally, the farmers grow their orchards through seeds. As a result, most of the loquat orchards do not possess the plants with uniform fruit characters and fruit is not of good quality. Previously no work has been reported regarding description of the loquat genotypes in Pakistan. The present study was, therefore, carried out to evaluate and characterize the available genotypes in the main loquat growing areas of Pakistan and to determine the genetic diversity among these genotypes. For this purpose, 9 sites were selected in the main loquat growing areas of Pakistan. Forty two genotypes were identified, which were compared on the basis of morpho-physical traits. Significant differences were observed with reference to various characteristics among different genotypes. Fruit weight of the genotypes ranged from 9.54 g (in HW4) to 47.84 g (in TB15). Range of flesh seed ratio was from 1.67 (in HW5) to 3.05 (in TB8). Minimum yield per tree was recorded as 25.85 kg (in TB15), while it was maximum (89.87 kg) in TB7. Correlations among some traits were also observed. Moreover, RAPD analyses of the genotypes were performed. Five RAPD primers gave reproducible results and generated 47 polymorphic bands. According to the dandrogram, two main groups of the loquat genotypes were identified with a linkage distance of 33%. For most of the locations, grouping of the genotypes was in accordance with the geographical locations. Out of the three genotypes from Mardan, one falls under the first group and the other two under the second group. The maximum number of genotypes (15) was identified at Takht Bhai, two of them belonged to the first group and 13 to the second group. Genotypes with good characteristics i.e. better yield, higher fruit size and weight, less number of seeds per fruit and higher flesh seed ratio can be recommended for further multiplication and introduction to the other loquat growing areas which would increase the income of farming community. The study also recommends establishing germplasm units in Punjab and NWFP and pooling all these genotypes for future strategies and breeding programs including selection, introduction, hybridization and mutation breeding. The present study would also be helpful for the documentation, management, and conservation of the loquat genetic resources of Pakistan.