Genomic DNA from the genotypes Khyber-87, Saleem 2000, Suleman-96, Pir Sabak-2004, Pir Sabak-2005, NRL- 0320, NRL–0517, RAS-II, Tatara, RAS-I, Bathoor, Fakhare Sarhad, Bakhtawar-94, Inqilab-91, Haider-2002, Noshera-96, and Auqab-2000 was amplified using RAPD primers Loci of 100-1400 bp sizes were amplified and on average 351 loci per genotype were amplified Average genetic diversity using the twelve RAPD primers ranged from 30-90% Phylogenetic relationship among the wheat genotypes was carried out using dendrogram analysis The seventeen genotypes were clustered in five groups It was found that the genotypes Pirsabak 2004 and Ras 1 were most distantly related to Khyber-87 It is suggested that these two genotypes be crossed with Khyber 87 for creating maximum genetic variations.