It might be thought that with the Portuguese having become, during the sixteenth century and beyond, such a considerable threat to the Islamic communities of the Indian Ocean and the trading web upon which those communities thrived, more attention might have been given to neutralising that threat. Putting aside the Ottoman and Persian empires, whose naval expeditions against the Portuguese have already been discussed, there was one other major Islamic empire during the age of fighting sail that could have turned itself into a significant maritime power in this region, that of the Mughals, an empire that dominated India from the mid-sixteenth century through to the early eighteenth century. While the Mughals did develop a navy, this based on the port town of Surat, with the vessels built there adopting European technical developments, on only a few occasions were these ships directly employed against the Portuguese or any other European navy. Instead, ships of the Mughal navy were invariably deployed in defending the empire against internal opposition. The Dutch and English, who could well have been viewed as a threat equal to that of the Portuguese, were seen as potential allies, for no other reason than that these two European nations had no more liking for the Portuguese than had the Mughals. In Surat, the British and the Dutch were permitted to build, maintain and repair ships, allowing the Mughals to gain an insight into methods of European ship construction.

It was with the EIC that the Mughals formed a particularly important alliance, ships of the Company sailing with Mughal traders for the purpose of safeguarding them from attack. Here the enemy was either the Portuguese or pirates from the west, the latter, in common with the Portuguese, possessing large, heavily-armed, square-rigged sailing ships. Antony notes that western pirates by the late seventeenth century had become quite numerous in the Indian Ocean, with Madagascar infamous as a pirate retreat and some Europeans going native and joining forces with indigenous sea raiders.