Twelve apricot (Prunus armeniaca L.) genotypes were collected from two valleys viz., Nubra (9,600 ft) and Leh (11,500 ft) of trans-Himalayan region of Ladakh (Jammu & Kashmir). These genotypes were characterized using random decamer RAPD primers. Initially, 20 decamer primers were used to screen the 12 accessions of which 16 produced the reproducible amplicons. These primers generated a total of 740 scorable bands with an average of 46.25 bands per primer of which 88.1% were polymorphic. The size of amplicon ranged from 250 to 2,100 bps. The resolving power of primer ranged from 3.5 to 15, whereas the polymorphic bands ranged from 4 to 10. The mean coefficient of gene differentiation (Gst) was 0.1072, indicating 89.28% of the total genomic diversity within populations. Estimated value of gene flow for RAPD (Nm = 4.164) indicated that there was very high gene flow among the populations. Similarity index value ranged from 0.49 to 0.84 indicating the high level of genetic diversity within the 12 apricot accessions. Genotypes from two valleys clustered into three non-specific groups with 4, 7 and 1 genotypes, respectively. Cluster I represented four genotypes of which three were from Leh and one was from Nubra valley. While, cluster II had seven genotypes of which five were from Leh while two are from Nubra valley. The third cluster consisted of only one genotype from Leh valley. The result showed high genetic diversity in apricot grown in Ladakh region of Jammu Kashmir.