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The genetic resources are useful only if they are exploited to create wealth for the nation. Therefore, detailed knowledge of genetic resources is essential for developing more efficient ways of evaluating and conserving biodiversity. All the buffalo breeds are recognized on the basis of their physical attributes and docility. But differentiation within the regional types is warranted as the phenotypes are insufficient to set clear boundaries between them. In view of this, the local buffalo population of Marathwada, named as Marathwadi was compared with known regional types like Nagpuri and Pandharpuri at molecular level using RAPD markers.