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Date palm is an important fruit crop of Pakistan with rich economic, social and nutritional values. The Baluchistan province of Pakistan has been well known for date palm cultivation since long. In addition to its long history of date palm cultivation, Baluchistan's geo-political position with Iran and Oman also highlights its position as a rich source of genetic diversity. The present study was aimed to estimate the genetic diversity and population structure of date palm in Makran division (Baluchistan), which is considered as a major groove for production of high quality date palm. A set of 52 microsatellite markers were utilized to analyze the genetic relationship among 61 date palm genotypes. High polymorphism was found with an average polymorphic Information content (PIC) of 0.67 which indicates significant genetic variation in date palm accession under study. A total 387 alleles were scored with an average of 8.23 alleles for each locus. According to the Bayesian clustering approach, the entire population was partitioned into two clusters i.e., Turbat and Panjgur with few admixture lines. The presence of two subgroups corresponded to distinct adaptive behavior of genotypes to different ecological environment. Analysis of molecular variance revealed 80% of the variation within individuals, while 16% was due to differences among individuals and 4% variation was found among populations. Principal coordinate analysis and neighbor joining tree exhibited the same clusters as illustrated in STRUCTURE V.2.2 software. The variation detected through SSR markers supports that Baluchistan region may be another center of diversity for date palm. The genetic diversity information from this study can also be used for future breeding programs, association mapping, gene cloning and germplasm conservation. [ABSTRACT FROM AUTHOR]