The chief problems now confronting the monarchy were no longer military, but social, economic and constitutional. The reign of Denis was not a period of uninterrupted peace. At the outset his legitimacy was disputed by his brother Afonso, and a brief civil war ensued. Hostilities between Portugal and the reunited kingdoms of León and Castile were terminated in 1297 by a treaty of alliance, in accordance with which Ferdinand IV of Castile married Constance, daughter of Dinis, while Afonso, son of Denis, married Beatrice of Castile, daughter of Ferdinand. A further outbreak of civil war, between the king and the heir-apparent, was averted in 1293 by the queen-consort Isabella of Portugal, who had married Denis in 1281, and was canonized for her many virtues in the 16th century. She rode between the hostile camps, and succeeded in arranging an honourable peace between her husband and her son.
These wars were too brief to interfere seriously with the social reconstruction to which the king devoted himself. At his accession the Portuguese people was far from homogeneous; it would be long before its component races "Moors and Mozarabs of the south, Galicians of the north, Jews and foreign crusaders" could be fused into one nationality. There were also urgent economic problems to be solved. The Moors had made Alentejo the granary of Portugal, but war had undone their work, and large tracts of land were now barren and depopulated. Commerce and education had similarly been subordinated to the struggle for national existence. The machinery of administration was out of date and complicated by the authority of feudal and ecclesiastical courts. The supremacy of the Crown, though recognized, was still unstable. It was Denis who initiated the needful reforms. He earned his title of the rei lavrador or "farmer king" by introducing improved methods of cultivation and founding agricultural schools. He encouraged maritime trade by negotiating a commercial treaty with England (1294) and forming a royal navy (1317) under the command of a Genoese admiral named Emmanuele di Pezagna (Manoel Pessanha). In 1290 he founded the University of Coimbra. He was a poet and a patron of literature and music. His chief administrative reforms were designed to secure centralized government and to limit the jurisdiction of feudal courts. He encouraged and nationalized the military orders. In 1290 the Portuguese knights of São Tiago (Santiago) were definitely separated from the parent Spanish order. The orders of Crato and of St Benedict of Aviz had already been established, the traditional dates of their incorporation being 1113 and 1162. After the condemnation of the Templars by Pope Clement V (1312) an ecclesiastical commission investigated the charges against the Portuguese branch of the order, and found in its favor. As the Templars were rich, influential and loyal, Dinis took advantage of the death of Clement V. to maintain the order under a new name; the Order of Christ, as it was henceforth called, received the benediction of the pope in 1319 and subsequently played an important part in the colonial expansion of Portugal.
Afonso IV adhered to the matrimonial policy initiated by Dinis. He arranged that his daughter Maria should wed Alfonso XI of Castile (1328), but the marriage precipitated the war it was intended to avert, and peace was only restored (1330) after Queen Isabella had again intervened. Peter, the heir, afterwards married Constance, daughter of the duke of Peñafiel (near Valladolid), and Afonso IV brought a strong Portuguese army to aid the Castilians against the Moors of Granada and their African allies. In the victory won by the Christians on the banks of the river Salado, near Tarifa, he earned his title of Afonso the Brave (1340). In 1347 he gave his daughter Eleanor in marriage to Peter IV of Aragon. The later years of his reign were darkened by the tragedy of Inês de Castro. He died in 1357, and the first act of his successor, Peter I of Portugal, was to take vengeance on the murderers of Inês.
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