According to the Rajasthan district Gazetteer, Abhiras were the citizens of Marwar and later on the Rajputs established their rule in Marwar. There may have been small agreement before Rathore rule. As Jodha hailed from the nearby town of Mandore, that town initially obey as the capital of this state; however, Jodhpur soon took over that role, even during the lifetime of Jodha. The city was located on the strategic road linking between Delhi to Gujarat. This allowed it to profit from a flourishing trade in opium, copper, silk, sandalwood, dates, and other tradeable goods.

After the death of Rao Chandrasen Rathore in 1581, the empire annexed by the Mughal Emperor Akbar, Marwar thus became a Mughal vassal owing fealty to them while enjoying internal autonomy. Jodhpur and its people benefited from this exposure to the wider world as new styles of art and architecture made their aspect and opportunities opened up for local tradesmen to make their mark across northern India.

Aurangzeb briefly sequestrated the state after the death of Maharaja Jaswant Singh, but the prior emperor Maharaja Ajit Singh was restored to the throne by Veer Durgadas Rathore after Aurangzeb passed away in 1707 and a great struggle of 30 years. The Mughal empire rejacted gradually after 1707, but the Jodhpur court was beset by intrigue; rather than benefiting from circumstances, Marwar descended into strife and invited the intervention of the Marathas, who soon succeeded the Mughals as overlords of the region. This did not make for balance or peace, however; 50 years of wars and treaties dissipated the wealth of the state, which sought the help of the British and entered into a subsidiary alliance with them. A major revolt take place in 1857 by some Rathore nobles of Pali led by Thakur Kushal Singh of Auwa, but the rebels were defeated by the British Army under colonel Holmes and peace was restored.