RAPD-PCR was carried out to, characterize the Malvi and Sahiwal breeds of cattle, using 17 operon series random primers, out of which 10 primers were found informative. Average number of polymorphic bands detected per primer was 8.57 and 7.85 in Sahiwal and Malvi breed, respectively. Size of polymorphic bands ranged between 200 and 2500 bp. Between breed band sharing (BS), value for these 2 breeds obtained was lower (0.43-0.66) than within breed BS value, which was 0.70-0.93 in Malvi breed and 0.68-0.88 in Sahiwal breed. A combined dendrogram based on Jaccard's similarity coefficient for both Sahiwal and Malvi breed indicated 2 distinct clusters, separating the Malvi and Sahiwal animals as 2 different breeds. Lower estimate of between breed genetic similarities indicated high degree of genetic diversity between these 2 breeds. This may be due to diverse origin and different purpose of raising these breeds. Malvi is raised for drought purpose while Sahiwal as milch breed. Breed specific markers were identified in both breeds.