The problem of the relation of the papal throne to the Greek clergy who remained within the Latin dominions is also interesting. It is known that a great number of bishops and the majority of the lower clergy did not abandon their places. In this case the pope held a conciliatory policy, allowing the Greek bishops to be ordained in the eparchies with an exclusively Greek population, and granting privileges concerning the preservation of the Greek rites and the church service, conceding, for example, the use of leavened bread for the Eucharist. However, the papal legates appeared in the Balkan peninsula and Asia Minor and tried to persuade the Greek clergy to join the union.
In 1204, a papal legate made the first attempt to obtain the consent of the Greek clergy to the recognition of the pope as the head of their church; the negotiations were held in St. Sophia, at Constantinople, and were of no avail. A very important role in the negotiations of that time was played by Nicholas Mesarites, later bishop of Ephesus, whose personality and activity were first elucidated by A. Heisenberg. In the years 1205-6 the negotiations continued their course. Nicholas of Otranto, abbot of Casole, of southern Italy, took part in them as an interpreter; holding the orthodox opinions, he recognized, like the whole church of southern Italy of that time, the papal primate and was an adherent of the union. Nicholas of Otranto, who has left many poems and prose works, almost all of them unpublished, deserves, as Heisenberg justly remarked, a special monograph.
The position of the Greek clergy became more complicated when in 1206 the patriarch of Constantinople, John Camaterus, died in Bulgaria, having fled there before the crusaders. With the permission of Emperor Henry, the Greek clergy of the Latin Empire applied to Innocent III for authorization to elect a new patriarch, and Henry allowed them to choose the patriarch provided they would recognize the overlordship of the pope. But the Greeks wished neither subordination to the Holy See nor reconciliation with it. Therefore nothing came of the disputation held at Constantinople, in the same year, 1206, when at the head of the Latins stood the Latin patriarch, Thomas Morosini and, leading the Greeks, Nicholas Mesarites. The Greeks of the Latin Empire began to turn to Theodore Lascaris. In 1208 a new Orthodox patriarch, Michael Autoreanus, was elected at Nicaea, who crowned Theodore Lascaris the Emperor of Nicaea. This was a fact of great moment not only for Nicaea, but also for the Greeks of the Latin Empire.
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Reference address : https://www.ellopos.net/elpenor/vasilief/ecclesiastical-relations-nicene-latin.asp?pg=2