Conflicts sometimes erupted between fishing vessels manned by southern Basques, from the Spanish Basque lands, and those manned by northern Basques, who were French. In 1554, the latter seized four ships from their Spanish cousins, off the coast of Newfoundland. The response was not long in coming. The same year, the Sancti Spiritu was transformed from a whaler into a privateer, lying in wait to ambush ships flying the French flag. A Spanish attack destroyed part of the French fishing fleet off Newfoundland. France and Spain were at war at the time and other skirmishes ensued. On April 21, 1557, King Philip II of Spain ordered that all vessels bound for Newfoundland, whether whalers, cod-fishing ships or others, be armed with at least four cannons and eight swivel guns. Some already were, such as the 130-ton Madalena, which had carried six cannons and eight swivel guns since 1550, and the 250ton San Nicolas, which was equipped that same year with six cannons and 12 swivel guns. The Santa Ana, a huge 650-ton ship, carried ten cannons and 20 swivel guns, while the San Juan, a vessel of about 300 tons which sank in 1565, was armed with eight cannons and ten swivel guns. In general, the galleons of the Spanish Basques were quite large, weighing between 200 and 650 tons and carrying crews of 50 to 120 men.
Documents of the time do not indicate the presence of soldiers, either on the ships or on land. However, officers and sailors could take up arms if needed, providing a kind of marine infantry. Every galleon carried iron artillery pieces, which supposes the presence of naval gunners. In order to train these men and ensure that the cannons were well maintained, the command of each ship included a gunnery officer.
Nevertheless, a document from 1571 related to a loan agreement for the construction of the 500-ton San Cristobal mentions that the outfitters should place on board 
this galleon 24 harquebuses, an equal number of crossbows and shields, 26 helmets, 20 breastplates and backs, and 144 small and large pikes, all to equip the 100 men on board. In the case of battle, the crew would be divided as follows: about half would use the harquebuses and crossbows, a quarter to a fifth would carry pikes and armour, and the rest would serve in the artillery or execute manoeuvres. To these armaments were added the personal weapons of the crew members and the officers: swords, daggers, and axes. This was not just an idle precaution. The San Cristobal, like all vessels of the period, ran a high risk of attack at sea. Furthermore, when the men landed they faced Inuit who were hostile because some Basques had carried off the wife of an Inuit chief around 1550. This ill-considered gesture would make the coast of Labrador, already rather forbidding with its bare rock and scraggy conifers, even more inhospitable for generations of Basque sailors.