This paper portrays the merge of Istria and Croatia within the context of the communist Yugoslavia after World War II investigating the relationship between the Catholic Church and the communist regime. The relationship between the Catholic Church and the regime in the political tensions during and immediately after the Second World War in Istria can best be viewed through the life and work of Božo Milanović, an example of a Croatian national priest of Istria. In the introduction, the process of the national integration of Croats in Istria in the second half of the 19th and the beginning of the 20th century under the leadership of the Croatian clergy is analyzed. Their national work was based on the priestly services for the people, the Christian teachings and the faith in God which demanded the rights for every person to possess dignity and the right of choice. After the years of fascism in Istria and the violent oppression of the Croatian people who represented the majority, the fight for national liberation under the leadership of communists seemed like a prime chance to establish a people’s government and resolving national disputes. After the impossibility of reshaping the borders through military means, politico-diplomatic solutions were the next step. The communists called upon the Istrian clergy to actively participate in the diplomacy understanding their important role amongst the people of Istria, as well as the need for them on an international level. These dynamics between the clergy headed by Milanović and the communist administration will be highlighted. Scilicet, these “unnatural” partners of sorts participate together in diplomacy as proponents of merging Istria into the newly created Yugoslavia despite the repression and the persecution the government enacted against the Church. After the Paris Peace Conference in 1947. and the merger of the “Zone B” to Yugoslavia, the Croatian clergy starts to passivize in political disputes, and the regime politics of repression increases in intensity in the fight against its greatest ideological opponent. This state of affair lasted until the London Memorandum in 1954. when the Church in Istria is stripped of many of its prior privileges unimaginable in other parts of Yugoslavia.