During the 13th century, the presence of numerous Christian Mongols in the Mongol court and army had many different ramifications. General statements to the effect that the Mongols were philo-Christian or that the Church and its hierarchy were not taxed during the domination are misleadingly inaccurate. While specific Mongols were philo-Chriatian, and though churches under the jurisdiction of certain naxarar families were not always taxed, the situation changed from ruler to ruler.
The earliest information on relations between the Mongols and the Armenian Church is found in Kirakos Ganjakec'i' History and relates to the first appearance of the Mongols in the Caucasus, ca. 1220/21:
...False information came concerning them to the effect that they were mages and/or of the Christian faith—wonder-workers—and that they had come to avenge the Christians from the tyranny of the Tachiks. And it was said that they had with them a portable tent-church and a miracle-working cross and that they would bring and throw an epah of barley before this cross and all the soldiers would take from it, and give it to their horses and the supply would not be exhausted...Such false rumors filled the land. Therefore the inhabitants of the country did not fortify themselves  in, to the point that one lay presbyter, taking his people, even went before [the Tatars] carrying [in procession] hooded crosses. The enemy put them to the sword, one and all (1).
The Mongols' motives in this instance, during their reconnaissance mission of 1220/21 simply may have been to terrorize the population. However it is not impossible that the unfortunate Christian welcoming party was mistaken for a band of secular princes. According to Kirakos Ganjakec'i, when in 1236 the Mongols returned to the Caucasus and in subduing the region captured the great cleric and scholar Vanakan vardapet, they thought that he was a secular prince and pressed him for information about fortresses and the whereabout of the Armenian lords (2). In any case, in 1236 the Mongols did not exterminate the intellectuals who had fallen into their hands. Vanakan,  his student Kirakos, and many other clerics were forced to serve the Mongols as secretaries, "writing and reading letters" (3).
A definite improvement in conditions for Christians of the Mongol Middle East was achieved by the Syrian doctor of the Church, Rabban in 1241/42. Thanks to  Raban's efforts, Nerses, kat'oghikos of Caucasian Aghbania/Aghuania, was taken to Chormaghun's wife, Altana:
...They gave [Nerses] gifts and an al-tamgha, so that no one would harass him, [and] they gave him a Moghal Tatar guide who took him throughout his dioceses in Aghbania. For a long while neither [Nerses] nor his predecessors had dared to circulate throughout the dioceses due to the blood-thirsty and bestial nation of Tachiks. Now [Nerses] passed throughout his dioceses, returning peacefully to his residence in Xamshi monastery (5).
In 1247/48, the kat'ogikos Kostandin of Cilicia sent to Greater Armenia gifts and money for the embellishment of the monastery of St. T'adeos, which was then elevated to a diocese. This rennovation work was entrusted to a vardapet Yovsep' and was expedited by the Mongols:
And Yovsep' went to a Tatar commander named Angurak noyin whose summer quarters were close by the tomb of the blessed apostle T'adeos. And on his command, Yovsep' blessed the church and held the pre-consecration ceremony, built a monastery and assembled many clerics in it.
The Tatar man enlarged the roads on all sides [so that] all pilgrims could come amongst his troops fearlessly. He commanded strictly that no one wishing to come be harassed, and he humbled himself to them with love. And many of them came and baptized their sons and daughters, and many who  were possessed by devils and were sick became healed, and the name of our Lord Jesus Christ was glorified (6).
To my knowledge, the implications of certain statements in the sources concerning the tax status of the Armenian churches have not been thoroughly understood. According to Step'annos Orbelean, prior to Smbat Orbelean's visit to the Far East in 1252/53, the churches of Orbelean Siwnik' were being taxed "bitterly" (7). In Monge-Khan's  presence, Smbat complained about the harassment of the churches (8), and received from Mongke "a decree freeing all the churches of Armenia and the priests", a statement repeated twice (9). With encouragement from Baiju's wife, Smbat rennovated Siwnik''s religious seat Tat'ew (then in a dilapidated condition) (10). Kirakos and the History of K'art'li very clearly state that as a result of emir Arghun's census of 1255, neither Church nor clergy was to be taxed (11). However, in 1257 When Hasan Jalal visited Batu-Khan in the North, he pointed out that Nerses, kat'oghikos of Aghbania/Aghuania, still was being harassed. He was given a written order that such harassment should stop (12).
 The fact that Hasan, subsequently "being harassed by tax-collectors and by [emir] Arghun" (13) was obliged to visit the Far East to complain, demonstrates the crucial point, and is equally valid for the secular Hasan and the clerical Nerses. It was not enough simply to have written patents of authority or protection. The local Mongol noyins did not always implement them.
In the late 1270's according to the History of K'art'li, the twelve retreats of Garesja, Georgia were taxed by the Mongols—even though under the administration of so loyal a Mongol supporter as Sadun Arcruni/Mahkanaberdeli (14). In the early 1280's (and presumably before), more than 150 Armenian monasteries within the Georgian state were being taxed (15). Consequently we must conclude that even before the Islamization of the Mongols, many Armenian churches were taxed.
William of Rubruck and Het'um the Historian provide valuable information regarding Armenian clerics in Asia and about Armenian Christian influence on the Khans. Rubruck, who travelled to the Far East during 1253-55, found Armenian priests at virtually all the major stopping places. At the very start of his trip, in Constantinople, he met and conversed with Armenian merchants and resident clerics (16). At Sarai on the Volga river, the capital of the Northern Tatars, he encountered at the court of Sartakh-Khan (Batu's son) "Armenian priests who knew Turkish and Arabic" and were employed as translators in addition to performing religious duties (17). Armenian priests were serving as translators in Qara Qorum, Mongolia, also as William subsequently discovered (18).
In Qara Qorum, Rubruck came upon a small Armenian chapel. Its colorful attendant was the "monk" Sargis. This  impostor claimed that:
...he had been a hermit in the country of Jerusalem, and that God had appeared to him three times, enjoining on him to go to the Prince of the Tartars. But as he neglected going, God threatened him the third time, striking him down to the ground, and saying that he should die if he did not go; and that he should say to Mongke-Khan that if he would become a Christian, all the world would come under his rule, and that the great Pope would obey him...(19).
Sargis indeed was an Armenian, "swarthy and lank" (20), but not a priest; and, if a Christian, of a rather shamanistic sort (21):
...but he lied, for he had taken no [religious] orders, and did not know a single letter, but was a cloth weaver, as I found out in his own country, which I went through on my way back (22).
Although William does not mention other Armenian clerics by names, he does allude to their presence. Thus, worried  that the Pope's letters he was carrying may have been tampered with, he wrote:
...I feared that as those who had interpreted your letters were Armenians from Greater Armenia—great haters of the Saracens—they had perhaps through hatred and for the discomfiture of the Saracens, gratuitously translated as had suited their fancy (23).Furthermore, Rubruck's comment that Armenian Easter was celebrated in Qara Qorum with a large clerical procession to the Khan's residence, only makes sense if there were a sizeable number of Armenian clerics present (24).
While in Qara Qorum, William encountered an unnamed Armenian lordly petitioner to Mongke-Khan:
A certain Armenian who had come with the monk had brought this said cross from Jerusalem, as he said, and it was of silver, weighing perhaps four marks, and had four gems in the angles and one in the center; and it did not have the image of the Savior, for the Armenians and Nestorians are ashamed to show the Christ fixed to the Cross. And they had presented it to Mongke-Khan, and Mongke asked him what he wanted. Then he said he was the son of an Armenian priest, whose church had been destroyed by the Saracens, and he asked his help to restore this church. Then [Mongke] asked him with how much it could be rebuilt, and he said two hundred iascot—that is two thousand marks. And he ordered that he should be given letters to him who receives the tribute in Persia and Greater Armenia, to pay him this sum of silver (25).
 In my opinion, the lord mentioned above probably was Smbat Orbelean, whose first trip to the Far East took place while William was in Qara Qorum.
Het'um the Historian's History provides an account of Armenian Christian influence in the courts of various Mongol Khans. Evidently, some of his information is fanciful or perhaps even wishful thinking. However, the unmistakable import of his narration is that Armenian Christians enjoyed considerable influence with different Khans. Supposedly, when king Het'um of Cilicia visited Mongke-Khan in the early 1250's:
...First he urged the Khan to convert to Christianity and to accept baptism together with his people; second, that eternal peace and friendship be established between Christians and Tatars; third, that it be possible to construct Christian churches in all of the Tatar countries and that the Armenians be freed from taxes and other burdens; fourth, that the Holy Land and the Holy Sepulcher be wrested from the Turks and given to the Christians; fifth, that the caliph in Baghdad, the head of the [Muslim] religion, be done away with...When the Tatar Khan had consulted with his princes and grandees, he replied to the king of Armenia: "I accept your requests. I shall accept baptism and adopt the Christian religion and show concern that all my subjects do likewise....(26)." 
Chapter 24 of the History is entitled "Regarding the Baptism of Mongke-Khan":
Now after Mongke had accepted the requests of the Armenian king with charitable munificence, he had himself baptized by the chancellor of the Armenian kingdom, who was a bishop. With him (were baptized) his house and numerous other esteemed and grand men and women (27).
The Cilician king Lewon (like all the Cilician kings) is elevated in Het'um's account to the position of defender of the Christians. When visiting Abaqa-Khan in Iran:
...the king of Armenia beseeched him regarding freeing the Holy Land from the infidels. And Abaqa so promised, simultaneously advising the Armenian king to send emissaries to the Pope and to the orthodox kings [regarding this matter] (28).
Thus we may conclude that an Armenian clerical presence existed at the courts of the Khans already by the early 1250's, and probably earlier. It may have developed into a sizeable presence before the Islamization of the Mongols in the late 13-early 14th centuries, involving clerics both from Greater Armenia and Cilicia. The influence of Christian Cilician kings with the Khans ended with Mongol Islamisation.
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