Gray langurs (Semnopithecus spp.) are leaf eating monkeys fragmentally distributed in northern hills of Khyber Pakhtunkhwa (KP) and Azad Jammu and Kashmir (AJK). It was believed that different fragmented populations of these monkeys might have experienced a genetic isolation or inbreeding. We assessed the level of genetic diversity and genetic isolation of different langur populations using Randomly Amplified Polymorphic DNA (RAPD) genetic markers. We collected 86 different samples (feces 64, hair 13, blood 5, tissues 4) from 5 geographic langur populations of Pakistan and Azad Jammu and Kashmir (AJK) and succeeded in extraction of DNA from 23 samples, which were used for further genetic analysis. RAPD makers (n=8) produced 245 bands (30.62±2.87 Mean±SE / primer) of different molecular weights (126-3342 bp), of which, 96 were population specific. Polymorphism was (37.71±5.29%; mean ± SE), with the highest in Muzaffarabad population (54.29%), followed by Poonch (43.67%) and Neelum (36.73%). Values of Shannon’s (I: 0.129-0.200) and Nei’s genetic diversity (He: 0.082-0.117) indices were low. Total heterozygosity (Ht: 0.144±0.007), genetic diversity within population (Hs: 0.096±0.005), between populations (Dst: 0.018±0.003), genetic differentiation constants among populations (Gst: 0.153±0.025) and within populations (Rst: 0.847±0.025) were calculated. Gene flow (Nm: 3.246±0.448) and genetic similarity (97-98%) between populations was high. UPGMA based dendrogram identified five distinct geographic groups, and Mantel tests (Rxy=-0.008, P>0.05) suggested a non-significant relationship between genetic distance and geographic distance. Phist (ΦPT) value suggested a significance difference in within population and between populations (PT=0.042; p=0.006) variances, suggesting that within populations variation was higher (96%) than variation between populations (4%). Present study suggested a low level of genetic diversity; however, gene flow was higher suggesting low chances of inbreeding between gray langur populations of Pakistan and AJK.