The paper discusses the difficult position of the Serbian Orthodox Church and clergy in Bosanska Krajina after the 1858 Rebellion in Krajina. Though the reforms introduced by the Porte granted the right to reconstruct and build new Orthodox churches, Muslim extremists hindered these initiatives in many towns and places, including Bosanska Gradiška, Bosanska Dubica, Prijedor, Banja Luka, Bihać, Bosanski Petrovac and Glamoč. The Rebellion in Krajina of 1858 left the Serbian Orthodox Church in Bosanska Krajina devastated. Dozens of churches were set on fire or torn down, including the two monasteries–pillars of the Orthodoxy in Bosanska Krajina–Rmanj from the 15th century and Moštanica from the 16th century. Many priests had been arrested or killed. The year later, in 1859, the Safer Order settled relations between the Turkish authorities and Serbs, however, the groups of powerful Muslim leaders continued to obstruct the attempts to reconstruct destroyed churches and build new ones. In the Bihać area, Tahir–bey Kulenović and Mustaj–bey Alajbegović from Kulen–Vakuf lead one such group and in Banja Luka Nazif–aga Djumišić. Later on, the relaxation of the Porte stands and political efforts of the deputy in the Orthodox Peoples’ Assembly in Constantinople Gavro Vučković Krajišnik in the 1860s and 1870s resulted in reconstruction of destroyed and construction of new churches in Bosanska Krajina, in Ramići near Ključ, Gorinja, Bukovača and Kolunić near Bosanski Petrovac, Bihać, Jezero near Bihać, Banja Luka, Stari Majdan, Oštra Luka near Stari Majdan, Glamoč, Bosanska Gradiška, Bosanski Novi, Hašani near Bosanska Krupa, Prijedor, Busnovi near Prijedor and Sanski Most. Monasteries Rmanj, Moštanica and Liplje from the 15th century near Kotor Varoš had been reconstructed. The Orthodox church started to stregthen its position with establishing of the Orthodox seminary in Banja Luka in 1866 that became the main defence from the Muslim extremism and, even more important, increasing Catholic proselitism.