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The challenge that Spain faced in the Mediterranean was very different from what the Portuguese faced in the Indian Ocean. In the former, Spain and her allies faced a very determined enemy in a venue where there was hardly any technological advantage. Mediterranean warfare was dominated by galleys, rowed by galley slaves, and fought largely on the decks of the vessels. In very few engagements did the Spanish side deploy the galleas, effectively a seaborne gun fort that had to be towed into position. The Spanish had an edge what with their Tercio soldiers, but this edge is not major. Finally, the Ottomans almost always had the advantage in numbers and determination, whereas the Doanish had to rely on a coalition that was often unreliable.
In the Indian Ocean, the Portuguese had decisive gunnery advantage, in particular in the high seas. They did not always win, but they were largely able to whittle down more numerous foes from afar, with little damage to their own fleet. The Spanish too enjoyed this advantage as they entered south east Asia through their outpost in The Philippines, but they rarely had need to confront a naval power there directly so this is rarely mentioned.