His fleet cruising off the coasts of Epirus held a central strategic position in relation to the still dispersed Christian fleets. The papal contingents on the western shores of Italy and the Spanish fleets in the ports of the Two Sicilies, or coasting from Spain by the Gulf of Lyons and the Italian shores, were, it is true, beyond his immediate reach, but he could easily lop off one important branch of the triple League by cutting off the Venetians. The squadron from Crete must pass him to the southward; the more important contingent from Corfu must pass between him and Southern Italy in narrow seas where he could hardly fail to bring it to action, and if it fought, the chances were he would overwhelm it. Or he might attack it at Corfu, or drive it from the island back upon Venice. If he had good luck he might hope to be in time even after this to strike a blow also at the Cretan squadron.
But he thought only of plundering and burning along the coasts, carrying off crowds of prisoners, some of whom were at once added to his crews of chained rowers. Veniero at Corfu had to steel his heart against entreaties to come to the rescue of the mainland coast population. He could not save them, and he dared not destroy his fleet in a hopeless effort. He must seize the opportunity while the Turks were occupied with their raids to sail unopposed to Messina. He decided even to risk the loss of Corfu. He was acting on the sound principle that in war all minor objects must be sacrificed to the chief end of the campaign. But he could not be sure that in obeying his original orders, and taking his fleet to Messina, he was not in another way risking his position, perhaps his life. He was leaving to the Turks the temporary command of the Adriatic. After he left Corfu they carried fire and sword along the Illyrian coast. There was a panic in Venice, and the city of the lagoons made hasty preparations for defence. But Veniero's action was soon justified. The news that the Christian armada was assembled at Messina alarmed Ulugh Ali into abandoning any further enterprises in the Adriatic, and his squadrons withdrew to join the concentration of the Turkish fleets at the entrance of the Gulf of Corinth.
It was not till 23 August that the Spanish Prince arrived at Messina, took command of the assembled fleets, and proceeded at once to organize his forces, and issued his sailing and battle orders.
Nearly three hundred ships crowded the harbour of Messina. There were three fleets, the Italian squadrons under the papal admiral Colonna, the Venetian fleet, and the fleet of Philip II formed of the ships of Spain and Naples. The main force of the three fleets was made up of galleys. But there were also six galleasses and some seventy frigates, the former depending chiefly, the latter entirely, on sail power for propulsion. The frigate was, in the following century and almost up to our time, what the cruiser is in the armoured navies of to-day. But in the Mediterranean fleets of the fifteenth century the frigata represented only an early type, out of which the frigate of later days was developed. She was a small sailing-ship, sometimes a mere yacht, armed only with a few light guns. The frigates were used to convey stores, the swifter among them being often employed as dispatch boats. Depending entirely on the wind, it was not always easy for them to accompany a fleet of galleys. Don Juan gave up the idea of making them part of his fighting fleet. It was still the period of the oar-driven man-of-war, though the day of sails was close at hand.
The six galleasses represented a new type, a link between the oared ships of the past and the sailing fleets of the immediate future. They were heavy three-masted ships, with rounded bows, and their upper works built with an inward curve, so that the width across the bulwarks amidships was less than that of the gundeck below. The frames of warships were built on these lines till after Nelson's days. This "tumble home" of the sides, as it was called, was adopted to bring the weight of the broadside guns nearer the centre line of the ship, and so lessen the leverage and strain on her framework. The guns had first been fired over the bulwarks, but at a very early date port-holes were adopted for them. The galleass had a high forecastle and poop, each with its battery of guns, pointing ahead, astern, and on each side. Other guns were mounted on the broadsides in the waist of the ship; and to command the main-deck, in case an enemy's boarders got possession of it, lighter guns were mounted on swivels at the back of the forecastle and on the forepart of the poop. Compared to the low, crowded galley, the galleass was a roomy and much more seaworthy ship. She was generally a slow sailer, but in order to enable her to make some progress, even in calms or against a head wind, and so work with a fleet of galleys, she had a rowers' deck, under her main or gundeck, and on each side twelve or fifteen oars of enormous length, each worked by several men. She had the drawbacks of most compromises. She could not sail as well as the frigate, and her speed with the oar was much less than that of the galley. But the gain was that she could be used as a floating battery, carrying many more guns than the few pieces mounted in the galley's bows. The galleass's guns were high above the water, and the galleys dreaded their plunging fire. Each of Don Juan's six galleasses carried some thirty guns of various calibres, and to defend their high sides against an attack by boarders, their fighting-men were chiefly arquebusiers.
In order to fuse the triple fleet of the Allies into one armada, and to avoid the risk of international jealousies, Don Juan proceeded to form his galleys into five squadrons, each made up of ships selected from the three fleets, so that none of these divisions could claim to act only for Rome, or Spain, or Venice.
The organization of the Christian armada may be thus summed up in tabular form:—
| Division. | Commander. | Galleys. | Sailing-ships. | |||
| Total | 202 | +76 sailing-ships = 278 ships in all. | ||||
| Vanguard | Juan de Cardona | 007 | Galleasses | 06 | ||
| Main line of battle | Left Wing | Agostino Barbarigo | 053 | Frigates | 70 | |
| Centre | Don Juan de Austria | 062 | — | |||
| Right Wing | Giovanni Andrea Doria | 050 | 76 | |||
| Reserve | Alvaro de Bazan, Marquis de Santa Cruz | 030 | These frigates sailed during the voyage as a separate squadron under Don Cesar d'Avalos. They were employed as storeships and tenders. | |||