Meanwhile Hernando Pizarro, the brother of Francisco, had sailed to Spain to report their success.  He returned with royal letters confirming the previous grants to Francisco and his associates, and bestowing upon Almagro a jurisdiction over a given tract of country, beginning from the southern limit of Pizarro’s government.  This grant became a fruitful source of dissension between Almagro and the Pizarros, each claiming as within his jurisdiction the rich city of Cuzco, a question which the uncertain knowledge of distances in the newly-explored country made it difficult to decide.

But the Spaniards had now for a time other occupation than the pursuit of their own quarrels.  The Inca Manco, escaping from the captivity in which he had lain for a time, put himself at the head of a host of Indians, said to number two hundred thousand, and laid siege to Cuzco early in February, 1536.  The siege was memorable as calling out the most heroic displays of Indian and European valour, and bringing the two races into deadlier conflict with each other than had yet occurred in the conquest of Peru.  The Spaniards were hard pressed, for by means of burning arrows the Indians set the city on fire, and only their encampment in the midst of an open space enabled the Spaniards to endure the conflagration around.  They suffered severely, too, from famine.  The relief from Lima for which they looked did not come, as Pizarro was in no position to send help, and from this they feared the worst as to the fate of their companions.  Only the firm resolution of the Pizarro, brothers and the other leaders within the city kept the army from attempting to force a way out, which would have meant the abandoning of the city.  At last they were rewarded by the sight of the great host around them melting away.  Seedtime had come, and the Inca knew it would be fatal for his people to neglect their fields, and thus prepare starvation for themselves in the following year.  Thus, though bodies of the enemy remained to watch the city, the siege was virtually raised, and the most pressing danger past.

While these events were passing, Almagro was engaged upon a memorable expedition to Chili.  His troops suffered great privations, and hearing no good tidings of the country further south, he was prevailed upon to return to Cuzco.  Here, claiming the governorship, he captured Hernando and Gonzalo Pizarro, though refusing the counsel of his lieutenant that they should be put to death.  Then, proceeding to the coast, he met Francisco Pizarro, and a treaty was concluded between them by which Almagro, pending instructions from Spain, was to retain Cuzco, and Hernando Pizarro was to be set free, on condition of sailing for Spain.  But Francisco broke the treaty as soon as made, and sent Hernando with an army against Almagro, warning the latter that unless he gave up Cuzco the responsibility of the consequences would be on his own head.  The two armies met at Las Salinas, and Almagro was defeated and imprisoned in Cuzco.  Before long Hernando brought him to trial and to death, thus ill requiting Almagro’s treatment of him personally.  Hernando, on his return to Spain, suffered twenty years’ imprisonment for this deed, which outraged both public sentiment and sense of justice.