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Yellow fever killed a third of Havana and many of SA's officials and citizens

Source: The Menendez Marquez Cattle Barony at La Chua and the Determinants of Economic Expansion in Seventeenth-Century Florida #163

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The conditions for large ranches in north-central Florida seemed to have been met. The provinces were pacified. In Potano, the largest district of Timucua province, there were some 3,000 Indians, enough to maintain the transportation network but not to compete for the grasslands. There were creole entrepreneurs who had access to the capital with which to acquire both labor and livestock. And there were markets: internal ones at St. Augustine and the smaller Florida garrisons, and external markets in Spain and in Havana, where the treasure fleet was outfitted. But, in addition, there had to be more Spanish citizens than were needed to maintain the St. Augustine garrison, and there had to be continuity. These two determinants of economic expansion into the hinterlands were about to receive a serious setback.

In 1648 Francisco Menendez Marquez complained that a clique of Basques, with the governor as their leader, were monopolizing trade and threatening his life because he was carrying out his responsibilities as treasurer. (Frco Menendez Marquez, February 18, 1648.) A year after the King received this letter, Francisco was dead. Typhus or yellow fever, which had carried off a third of the people of Havana, had been brought from there to Florida. In St. Augustine the epidemic killed Francisco and his fellow treasury official, the governor, both company captains, and many friars. (Po Beltrin Santa Cruz, November 20, 1655.) [Note: The "fiebres putridas" were brought to Cuba on the New Spain flota in the spring of 1649.] Florida's Spanish population was so reduced that expansion would not be possible for years unless more settlers arrived on the scene. 
(Bushnell MM)