This paper highlights the impact of Pakistani minority migrants on the rural scenario in Jaisalmer district of Rajasthan. Nicknamed as ‘The Golden city’, it is situated in the western part of Rajasthan. Lying in the heart of the Thar Desert, it is the largest district of Rajasthan with a population of about 669919 persons. The length of international border attached to Jaisalmer District is 471 km (293 mi). The region is well known for its hard climatic condition. This region has been under turmoil and chaotic political conditions. After the war of 1965 and 1971 many Pakistani Hindu minority migrants have migrated to the western parts of the nation settling specially near the Radcliff Line. Research indicates that in Jaisalmer, the rural population percentage is 86.71%. Jaisalmer, Sam and Sankdathese are three panchayat samitee here. Survey reveals that the pakistani migrants in Jaisalmer have mainly settled in Nachana. Transport nagar, Gaffur Bhatta and Shree Mohangarh are the three main locality of migrants here. Though tourism is a major industry and the key attraction in Jaisalmer still, the rural population of the area suffers due to unemployment and illiteracy mainly. Many rural people are involved in illegal activities like drug smuggling, illegal migration or work as spy etc. Recently Jaisalmer police had caught some people working as a Pakistani agents, leaking confidential information to Pak army. This may be a big risk to our nation’s security. The ‘Ujas’ and ‘Seemantlok Sangtan’ are working for developing and supporting the migrants here also making efforts for getting Indian citizenship.