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Expulsion of Moriscos and Morisco conversos

The Inquisition searched for false or relapsed converts among the Moriscos, who had converted from Islam. Beginning with a decree on 14 February 1502, Muslims in Granada had to choose between conversion to Christianity or expulsion. In the Crown of Aragon, most Muslims faced this choice after the Revolt of the Brotherhoods (1519–1523). The enforcement of the expulsion of the Moriscos was implemented unevenly, especially in the lands of the interior and the north. In these regions coexistence had lasted for over five centuries and Moriscos were protected by the population; in many cases expulsion orders were partially or completely ignored.

The War of the Alpujarras (1568–71), a general Muslim/Morisco uprising in Granada that expected to aid Ottoman disembarkation in the peninsula, ended in a forced dispersal of about half of the region's Moriscos throughout Castile and Andalusia as well as increased suspicions by Spanish authorities against this community.

Many Moriscos were suspected of practising Islam in secret, and the jealousy with which they guarded the privacy of their domestic life prevented the verification of this suspicion. Initially, they were not severely persecuted by the Inquisition, experiencing instead a policy of evangelization a policy not followed with those conversos who were suspected of being crypto-Jews. There were various reasons for this. In the kingdoms of Valencia and Aragon, a large number of the Moriscos were under the jurisdiction of the nobility, and persecution would have been viewed as a frontal assault on the economic interests of this powerful social class. Most importantly, the moriscos had integrated into the Spanish society significantly better than the Jews, intermarrying with the population often, and were not seen as a foreign element, especially in rural areas. Still, fears ran high among the population that the Moriscos were traitorous, especially in Granada. The coast was regularly raided by Barbary pirates backed by Spain's enemy, the Ottoman Empire, and the Moriscos were suspected of aiding them.

In the second half of the century, late in the reign of Philip II, conditions worsened between Old Christians and Moriscos. The Morisco Revolt in Granada in 1568–1570 was harshly suppressed, and the Inquisition intensified its attention on the Moriscos. From 1570 Morisco cases became predominant in the tribunals of Zaragoza, Valencia and Granada; in the tribunal of Granada, between 1560 and 1571, 82% of those accused were Moriscos, who were a vast majority of the Kingdom's population at the time. Still, the Moriscos did not experience the same harshness as judaizing conversos and Protestants, and the number of capital punishments was proportionally less.

In 1609, King Philip III, upon the advice of his financial adviser the Duke of Lerma and Archbishop of Valencia Juan de Ribera, decreed the Expulsion of the Moriscos. Hundreds of thousands of Moriscos were expelled. This was further fueled by the religious intolerance of Archbishop Ribera who quoted the Old Testament texts ordering the enemies of God to be slain without mercy and setting forth the duties of kings to extirpate them. The edict required: 'The Moriscos to depart, under the pain of death and confiscation, without trial or sentence... to take with them no money, bullion, jewels or bills of exchange.... just what they could carry.' Although initial estimates of the number expelled such as those of Henri Lapeyre reach 300,000 Moriscos (or 4% of the total Spanish population), the extent and severity of the expulsion in much of Spain has been increasingly challenged by modern historians such as Trevor J. Dadson. Nevertheless, the eastern region of Valencia, where ethnic tensions were high, was particularly affected by the expulsion, suffering economic collapse and depopulation of much of its territory.

Of those permanently expelled, the majority finally settled in the Maghreb or the Barbary coast. Those who avoided expulsion or who managed to return were gradually absorbed by the dominant culture.

The Inquisition pursued some trials against Moriscos who remained or returned after expulsion: at the height of the Inquisition, cases against Moriscos are estimated to have constituted less than 10 percent of those judged by the Inquisition. Upon the coronation of Philip IV in 1621, the new king gave the order to desist from attempting to impose measures on remaining Moriscos and returnees. In September 1628 the Council of the Supreme Inquisition ordered inquisitors in Seville not to prosecute expelled Moriscos "unless they cause significant commotion." The last mass prosecution against Moriscos for crypto-Islamic practices occurred in Granada in 1727, with most of those convicted receiving relatively light sentences. By the end of the 18th century, the indigenous practice of Islam is considered to have been effectively extinguished in Spain.