After the death of Djuradj Crnojevic, Zeta/Crna Gora was ruled by his brother Stefan, who was a Turkish vassal. In the new administrative division of Balkan, Montenegro was a part of the Skadarski Sandzakat(1499-1514). During this period, while Brda and North-West of Montenegro were nominally independent, the part of Montenegro under the mountain Lovcen (Podlovcenska Crna Gora) remained entirely independent (D. Zivkovic, Istorija Crnogorskog Naroda, Cetinje, 1989). By the end of XV century Upper Zeta comprised Katunska, Rijecka, Crmnicka, and Ljesanska nahias, and the name of Crna Gora (Montenegro) was widely in use. The borders of Montenegro at the beginning of XVI century were as follows: 

South-mountain Sutorman, hills between Crmnica and Pastrovici, than, Pastrovici, Majina, Brajici, and Pobora to the Adriatic sea near Grbalj; 

West-from the Walls of Kotor town, above Dobrota, Ljuta, Orahovac, Drazevina, Perast, Risan and Ledenica; 

North-over river Sitnica, than between Grahovo and Cuce and towards Pusti Lisac: 

East-mountain Lastva, Garac, than hills over Susica, than below Komani to Ljeskopolje, than above Zabljak and Dodosi, and over the Lake of Shkodra (Skadarsko) to Sutorman (J.Jovanovic,1948, Stvaranje Crnogorske Drzave i Razvoj Crnogorske Nacionalnosti, 1948, Cetinje, p. 60-61). 

In 1514, Montenegro was proclaimed as the separate Crnogorski sandzaktat, by order of Sultan Bajazit II. For the first Sandzak-beg was chosen Ivan Crnojevic's son Skenderbeg, who was a convert to Islam, and governed until 1528. Despite Skenderbeg's emphasized cruelty, Turks did not have real power in Montenegro. The real power was in the hands of tribal (plemenskih) heads. From 1534 onwards, there is no more mentioning of Crnojevics in Crna Gora(J.Jovanovic,1948, Stvaranje Crnogorske Drzave i Razvoj Crnogorske Nacionalnosti, 1948, Cetinje, p. 54-55).

The year 1516 saw a shift in the constitution of Montenegro that many historians regard as having ensured its survival as an independent state. The last of the Crnojevic dynasty retired to Venice (he had married a Venetian) and conferred the succession upon the bishops of Cetinje. In Montenegro the position of vladika, as the prince-bishop was known, brought stability to that country's leadership. The link between church and state elevated it in the eyes of the peasantry, gave it an institutionalized form of succession that prevented its becoming a matter of contest between minor chieftains, and excluded the possibility of compromising alliances with the Turks. 

In this period, vladikas came from different families and were elected by popular assemblies. According to St.Petar Cetinjski "The Vladika is an exemplary Montenegrin, as were the first Vladikas, and he cannot be but a born Montenegrin from one of the best Montenegrin families. A renown writer of a history of Montenegro noted: "The Vladikas were true spiritual and popular leaders of the Montenegrin people. The Vladika was a guardian of the people's spiritual strength and self-awareness, based on faith and the tradition of heroism and glorious ancestors...the Vladikas governed not by brute force but by purely moral influence, persuasion and prayers. And they all recognized the supreme authority of the Faith and the Church in which the Vladikas and the people were one. It was a special kind of spiritual brotherhood " (Rovinski, Crna Gora u proslosti i sadasnjosti, 1989, Cetinje, 352-3). 

The institution of the theocratic sovereign and the individuals who occupied it through the centuries were key to Montenegro's independence, the Montenegrin national identity and unity, against the backdrop of tribal divisions. Surrounded by the Ottoman empire, nestled in the highlands around the Mount Lovcen, Montenegro kept its sovereignty through the leadership of the vladikas. 

Therefore, diocese of Cetinje, having overcome the phase of a passive onlooker, took active, and even leading political role in the fight for liberation against Turks. At the beginning of XVII century, Montenegrins fought and won two important battles against Turks on Ljeskopolje (1603 and 1613), under the leadership and command of Cetinje's metropolitan, Rufim II Njegus (D. Zivkovic, Istorija Crnogorskog Naroda, Cetinje, 1989). This was the first time that the Turks were defeated under the leadership of a Cetinje's vladika, and that became tradition thereafter. At the same time this signify the beginning of the factual autocephalic activity of Montenegrin Orthodox Church, institutionalized in the diocese of Cetinje (D. Zivkovic, ibid.). 

During XVII century, Montenegrins gained on confidence fighting the mightiest army of the time. Turkish forces suffered many defeats in the hands of Montenegrins who not only kept their independence but progressively reasserted their sovereignty over neighboring territories.

Nevertheless, this period was a difficult one for the small, landlocked Montenegrin state, which was almost constantly at war with the Ottoman Empire. Cetinje itself was captured in 1623, in 1687, and again in 1712. Three factors explain the failure of the Turks to subdue it completely: 

• the obdurate resistance of the population, 
• the inhospitable character of the terrain (in which a cynic may say that "a small army is beaten, a large one dies of starvation"), and 
• the adept use of diplomatic ties with Venice. 

During the reign of Danilo two important changes occurred in the wider European context of Montenegro: the expansion of the Ottoman state was gradually reversed, and Montenegro found in Russia a powerful new patron to replace the declining Venice. The replacement of Venice by Russian patronage was especially significant, since it brought financial aid (after Danilo visited Peter the Great in 1715), modest territorial gain, and, in 1789, formal recognition by the Ottoman Porte of Montenegro's independence as a state under Petar Petrovic Njegos (Peter I).

The ebbing of the Ottoman tide proved significant for Montenegrin religious identity, which appears to have been particularly unstable throughout the 18th century. In order to preserve their own identity and enforce the established theocratic, Orthodox state, Montenegrins organized the legendary mass slaughter of those who had converted to Islam on Christmas Eve 1709 (the "Montenegrin Vespers''). The decline of Turkish power help Montenegrins to gradually stabilize and eventually strengthen Montenegro's Orthodox identity. Catholicism retained a toehold in the area, and only recently have Catholics identified themselves as Croats. 

The vladika's rule in this mountanious principality, which lasted until the middle of 18th century, when secular Western ideas intruded, is described in the literature as Europe's closest  approximation to Tibet: a theocracy, ruled by celibate orthodox prince bishops selected from the boys of the Njegusi tribe, who lived in the stony valleys south of Cetinje.