Pakistan is blessed with a wide range of indigenous mango germplasm. These mango genotypes, growing at Punjab and Azad Jammu and Kashmir (AJK) and its vicinity are valuable resource for unique genetic diversity. This germplasm has declined drastically due to population pressure, deforestation and high incidence of insect pests and diseases including Mango Quick Wilt Disease (MQWD). Hence, the aim of this study was to develop DNA fingerprints and determine the genetic diversity of the availabale germplasm. On the other hand, better understanding about the varability of MQWD pathogen is also important for incorporating resistant traits in the plant. Therefore, DNA profiles of 232 genotypes of Pakistan were developed with 114 SSR markers to determine the population structure. SSR based genetic diversity analysis identified a total of 593 alleles ranging from 2 to 18 alleles per locus, which were able to distinguish almost all of these genotypes. The average polymorphism information content value was 0.665. The expected and observed heterozygosity values were 0.695 and 0.619, respectively, which exhibited moderate level of genetic diversity among mango genotypes. Thirty unique alleles were identified in commercial and some wild genotypes. This analysis identified 26 duplicate entries in the collected samples, though they were identified as different genotypes at the time of sampling. The remaining genotypes (203) were found to be genetically distinct from each other. The Bayesian cluster, principal coordinate and hierarchical clustering analyses divided the collected genotypes into three groups i.e. A, B and C. Groups A and C consisted of entirely indigenous genotypes, while all commercial genotypes were clustered in group B. The genotypes from AJK have relatively broader genetic base within their clusters as compared to the genotypes collected from Punjab. However, strong correlation between geographic distribution and genetic clustering suggested no extensive exchanges of mango germplasm across these geographic areas. The genetic diversity of Pakistani genotypes was found to be higher when compared with the genotypes of other mango growing countries of the world. No association could be established between the embryony and SSR markers analyzed. The analysis identified the mislabeling of the introduced genotypes from other countries. These markers also identified and confirmed the parentage of hybrid genotypes. Most of the genotypes collected from Rahim Yar Khan, Multan and Khanewal showed close relationship with ‘Chaunsa’, ‘Sindhri’ and ‘Langra’. Another aspect of this study was to assess the genetic diversity of the casual agent of the most notorious mango disease, MQWD, which is a major threat to mango production in Pakistan. Eighteen fungal isolates were sampled from infected mango decline trees from mango growing areas of Punjab. The genetic makeup of these isolates was determined by using various DNA marker genes like ITS, β-tubulin and EF-1α. The comparison of their nucleotide sequencing data showed that ‘RYK-147’ belongs to Ceratocystis manginecans; while, rest of the seventeen samples belong to Ceratocystis fimbriata. These results are contradictory to the previous reports, which showed that disease causing fungi belongs to solely C. manginecans. This study showed that the mango decline disease is caused by both fungal species. However, the C. manginecans, isolated in this study has the same genetic makeup as previously reported from Pakistan and Oman. This contradiction in results is likely due to sampling from the regions, which are different from the previous studies in Pakistan. The genetic diversity analysis of 18 isolates was also carried out through 20 SSR markers. The results indicated that the isolates collected from Multan, Khanewal and Muzaffargarh are genetically similar. While, low level of genetic diversity was observed among isolates sampled from Rahim Yar Khan. The analysis also screend out C. manginecans, as a causal agent of mango wilt disease in isolate of ‘RYK-147’. These all isolates were sampled from commercial mango genotypes, which have low level of genetic diversity. High level of genetic similarity in the disease causing fungi might be an evolutionary outcome of diversity relation between host and pathogen. The quantitative analysis of the genetic diversity and population structure would help cultivar improvement in the future mango breeding programs.