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The Latin Kingdom of Jerusalem was established, and the knights of the Holy Sepulchre played an integral role in advancing peace in the territory. The Muslim attacks, however, did not cease, and defense of the Basilica of the Holy Sepulchre which was built by the earliest knights of the Order and still stands today, covering both the site of the crucifixion of Christ and His burial place became impossible.
The earliest band of knights fled to the city of Acre, to the fortress of St. John, where they were received by other groups of besieged crusaders. They remained there from 1245 until the great fortress fell to the Muslims in 1291, ending the Latin Kingdom of Jerusalem. A diaspora then took place among the Christians in Palestine. Many of the knights of the Holy Sepulchre remained in the Mediterranean basin; others fled as far as France and Spain. The works of the Order continued as far away as Poland, where knights had settled and later their descendants continued in the spirit of the defense of Christianity.
The activity of the Order, indeed its identity, in Palestine shifted from the knights, who returned to their own countries, to the religious Order of St. Francis, which had custody of the monastery of Mt. Zion. This group of Franciscans preserved the mission of the crusading knights of the Holy Sepulchre for centuries, mindful of the original bulla of appointment that entrusted the basilica, as well as the faithful, to the order's protection.
In 1330, Pope John XXII named the prior of the Franciscan house Custodian of the Order of the Holy Sepulchre. The custodian served as deputy to the pontiff, who reserved unto himself the governing authority of the Order, and yet, the custodians, in all effect, were responsible for all aspects of the Order's growth and governance, including the calling of new knights.