The Rathore Rajputs moved to Marwar - 'the region of death' in 1211 when they were defeated by Muhammad Ghori at Kannauj. Rao Jodha, the Rathore chieftain was forced to leave the former Rajput capital at Mandore in 1459, as the place was not located strategically. They chose a new place, located 8 km from the Mandore on the edge of Thar Desert. Rahores controlled a large part of Rajasthan, especially during the reigns of Rao Udai Singh (1581 AD) and his son Raja Sur Singh ((1595), who conquered Gujarat and a good part of Deccan for the Mughal Emperor Akbar.

The Rathores always had good relationships with the Mughals and Maharaja Jaswant Singh (1678) supported Shahjahan in the Mughal struggle for war of succession. Only problematic relationship they had was with Aurangzeb. After the death of Aurangzeb in 1707, Maharaja Ajit Singh became the ruler of Jodhpur. He drove out Mughals from Ajmer and added substantially to the Mehrangarh Fort.

The city of Jodhpur prospered because of its location on the strategic Delhi - Gujarat trading route.