In the mid 13th century, the Eastern Orthodox Serbian King Stefan Uroš I expelled its bishop Salvio, who took refuge in the Republic of Ragusa.

At first, he found a refuge in the Republic of Ragusa, and was given care over the Benedictine monastery at the isle of Lokrum, where he was a monk before becoming a bishop.

His successor, Bishop Sabin Cvjetković also occasionally lived in Mrkan, but due to pillages from hajduks and pirates during the Cretan War, mostly spent time in Dubrovnik.

Because of that, the Holy See requested from the new bishop Scipion de Martinis to take a vow that he would live on the territory of his diocese, which he did.

However, in the summer of 1664, Martinis reported that the hajduks ransacked the isle of Mrkan and pillaged and burned the church and the episcopal residence.

[10] Finally, through the diplomatic efforts, the Diocese of Trebinje–Mrkan was put under the administration of the bishops of Dubrovnik for an indefinite time by Pope Gregory XVI's bull Apostolici nostri muneris on 12 September 1839.

Thus, the Holy See decided on 21 October 1855, to give a right to officiate chrism to the Italian Jesuit Vincenzo Basileo, who previously served as a missionary in Neumski Gradac.

In the bull Ex hac augusta of Pope Leo XIII, it was designated that the diocese will be administered by the bishops of Dubrovnik, until otherwise be ordered.

[11] The Diocese of Trebinje–Mrkan suffered heavily during the Herzegovina uprising between 1875 and 1877; many Catholics and priests fled the area, and houses and churches were destroyed.

[14] The Catholics of Trebinje–Mrkan became frustrated with the lack of material aid from the new authorities and the inactivity of the new Bishop of Dubrovnik Mato Vodopić.

[15] Provicar of Trebinje–Mrkan Lazar Lazarević wrote to the Propaganda in Rome on 11 June 1887, again requesting the appointment of a new bishop and protection of Catholics from the new authorities.

[13] In mid-1887, Lazarević also wrote to the Austrian-Hungarian government in Sarajevo about Buconjić's encroachment in Trebinje–Mrkan but his petition drew no positive response.

Cardinal Luigi Galimberti, the new Nuncio in Vienna, started negotiations with Foreign Minister Count Gustav Kálnoky and showed him Rampolla's letter.

[18] On 5 September 1888, the clergy of Trebinje–Mrkan again asked Nuncio Galimberti for the new bishop and for Buconjić to respects the boundaries of Trebinje–Mrkan as established in the 1881 bull Ex hac augusta.

[19] On 17 June 1889, the Austrian-Hungarian government in Sarajevo and the Joint Ministry of Finance presented their proposal to Galimberti, in which they suggested the Bishop of Mostar-Duvno should administer Trebinje–Mrkan.

[21] The Austrian-Hungarian government also requested the Bishop of Mostar-Duvno, even though just an apostolic administrator, should have a regular jurisdiction in Trebinje–Mrkan and that he could appoint Franciscans to priestly duties.

[21] On 16 June 1890, the Propaganda decreed the bishop of Mostar-Duvno would administer Trebinje–Mrkan and the pope confirmed this decision on 8 July the same year.