While it can be argued that European armies carefully selected the opponents they would face, the same cannot be said of European navies. The accomplishments of the armies of Cortés and Pizarro in the Americas notwithstanding, the true military advantage held by Europeans over the rest of the world during the fifteenth and sixteenth centuries was their maritime superiority. European ships dominated the sea lanes. Few states outside Europe possessed the financial and material resources to construct and maintain naval forces similar or equal to those deployed by the Portuguese and Spanish.

However, the Ottoman Empire remained one power that European nations did not wish to challenge on land or at sea. Indeed, it has been suggested that Portugal's search for a sea-route to Asia was undertaken precisely because European military forces were loath to challenge the Ottomans on land. The Ottoman Empire was a land-based power and did not challenge Europe's maritime superiority. Portugal's naval dominance in the Indian Ocean was openly challenged by two Turkish raiding flotillas in 1551-1552 and again in 1585-1586. In 1551, a raiding party, led by Turkish admiral Piri Reis and consisting of twenty-three galleys, sacked Muscat and besieged the Portuguese castle at Ormus. In 1585, an adventurer by the name of Mir Ali Bey, with one poorly-armed ship, managed to sweep the Portuguese from the entire Swahili coast, with the exception of Malindi, and captured twenty Portuguese ships and accompanying booty.

Of the two Iberian powers, Portugal was undoubtedly the weakest. Portugal simply did not possess sufficient manpower and material to sustain a large standing maritime fleet. C.R. Boxer points out that at the height of Portugal's naval supremacy in the 1530's, Portugal did not posses more than 300 ships. The conquest of an empire helped the Portuguese by providing much-needed access to raw materials, such as teakwood from India. Unfortunately, these ships constructed from Indian teakwood were slow and very expensive to build and difficult to replace. Portuguese shipping in Asia was, therefore, increasingly handled by Asian seamen working under the direction of a few Portuguese officers. Indeed, there is evidence to suggest that Portuguese sailors were poorly-prepared to sail in the Red Sea in 1539. One merchant who was preparing an expedition, D. Go de Castro, found that none of the Portuguese pilots available to him were familiar with the straits of Bab-el-Mandeb. Perhaps more importantly, none of these Portuguese sailors possessed adequate charts of that region, forcing Castro to rely on "Arab, Gujarati and Malabar pilots" who were to bring their own nautical charts to guide the European ships. Nevertheless, as serious as these problems may have been, they did not inflict serious damage on Portugal's ability to dominate the Indian Ocean. Turkish, Egyptian, or Malayan corsairs in oared galleys posed no serious threat to the massive, and well-armed, galleons that comprised the core of Portugal's deep-sea fleet.

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