Mango (Mangifera indica L) belongs to the Anacardiaceae family, well known for enclosing the fruits of special traits such as cashew. Pakistan is a good producer of mango after citrus fruits with total 167.5 thousand hectares cultivated area with 1,732 thousand tons annual production. The country is contributing 8.5% of world mango trade (Nazish et al., 2017). Punjab and Sindh are two top mango producing provinces of Pakistan. The Punjab province’s districts spearheading in mango production are Multan, Rahim Yar khan, Bahawalpur and Muzzafargarh. Some popular and exportable varieties grown in the region are Sindhri, Black Chaunsa, Sammar Bahisht, Sufaid Chaunsa, Chenab Gold and Azeem Chaunsa. Mango germplasm studies are desirable in horticulture to characterize its morphological traits. There is an ambiguity in validating the parentage of genotypes. Therefore, it is important to understand the link between genotypes before starting any breeding program so that appropriate parents can be selected (Krishna & Singh, 2007). Breeding in mango is complicated due to long-term factors such as heterozygosity, low fruit set, polyembryonic behavior, long duration of evaluation, juvenility and out crossing behavior. Moreover, the conventional methods of parent selection are slow and ambivalent (Ravishankar et al., 2015). Nonetheless, the use of molecular markers in identifying parents has high efficiency and authentic predictability. Mango breeding is affected due to lack of genome sequence as there is limited information about the markers present in mango genome and the application of molecular technologies is limited in mango breeding programs(Kuhn et al., 2017). Molecular characterization is considerable and reliable due to advantageous properties such as less time consumption and high accuracy. Similarly, the results obtained by molecular investigation are more authentic. It helps to identify those useful traits which are costly and difficult to observe. Markers base identification of polymorphism is helpful because it targets specific gene and minimize the change of linkage lose during recombination(Dillon et al., 2014).Molecular markers are available is many types depending on their application and ability to identify genomes such as Randomly Amplified Polymorphic (RAPD), Amplified Fragment Length Polymorphism (AFLP), Polymerase Chain Reaction (PCR) based markers and Simple Sequence Repeat (SSR) (Bukhari et al., 2022). PCR markers are used for genetic diversity analysis. Likewise, RAPD, AFLP and SSR are frequently used for investigative purpose. SSR markers are preferred due to their ability to identify co-dominance, reproducibility, multiallelic nature, high relative abundance, auto-mutation, chromosomal location and authentic genomic coverage (Gupta, Kumari, Muthamilarasan, Parida, & Prasad, 2014). In mango genetic variability, SSR markers are frequently used because of complex nature of mango genome, so short sequences are more handy for its characterization (Shamili, Fatahi, & Hormaza, 2012). Therefore, SSRs are useful in mango genome sequencing studies due to their characters, which can be utilized for the fruit’s improvement within short duration and enhancing its genome accessibility for other molecular techniques (Mahato et al., 2016).As stated earlier, morphology is influenced by environmental conditions; thereby, morphological studies do not truly showcase genotypic representation of a specie. Moreover, apart from its arduous nature and uncertain results, morphological identification is a time-consuming process to get desired characters on later ages of the plant. We cannot differentiate limited polymorphism by using morphological and protein markers. However, genetic markers are helpful to identify polymorphism among the species (Bukhari et al., 2022). In this connection, a study was devised to find out genetic diversity among thirteen mid season Pakistani mango varieties to find the unique fingerprints among them that can aid in charting out futuristic breeding programs in the country.