According to one of the theories the Gagauz descend from the Seljuk Turks that settled in Dobruja (Bulgarian: Dobrudzha (Добруджа); Turkish: Dobruca; Romanian: Dobrogea) alongside the Pechenegs, Uz (Oghuz) and Cuman (Kipchak) people that followed the Anatolian Seljuk Sultan Kaykaus II (1236-1276). More specifically, one clan of Oghuz Turks migrated to the Balkans during the inter-tribal conflicts with other Turks. After settling in the eastern Balkans (Bulgaria) this clan converted from Islam to Orthodox Christianity in the 13th century and became known as "Gagauz Turks".
There are other theories about the origin of the Gagauz. According to some authors, they are descendants of Turkic Bulgars, a seminomadic people, who gave their name to present Bulgarians . According to another theory, most of the Gagauz are descendants of Orthodox Christian Greeks who adopted their Turkic language during the Ottoman rule of Anatolia like the Karaman Greeks of Konya. The other opinions connected the question about the origin of Gagauz with Oghuz, Pechenegs or Cumans.
Turkic-speaking tribes of the Nogai Horde inhabited the Budjak region of southern Bessarabia from the sixteenth to eighteenth centuries. Before 1807, a portion of these tribes were forced to abandon the Budjak by the Tsarist government of Russia, resettling in Crimea, Azov and Stavropol.
Between 1820 and 1846, the Russian Empire allocated land to the Gagauz and gave them financial incentives to settle in Bessarabia in the settlements vacated by the Nogai tribes. They settled in Bessarabia along with Bulgarians, mainly in Avdarma, Comrat (or Komrat), Congaz (Kongaz), Tomai, Cismichioi and other former Nogai villages located in the central Budjak region. Originally, the Gagauz also settled in several villages belonging to boyars throughout southern Bessarabia and the Principality of Moldavia, but soon moved to join their kin in the Bugeac. Until 1869, the Gagauz in Bessarabia were described as Bulgarians. During the Rumanian rule of Bessarabia (1856-1878), they supported Bulgarian schools in their settlements and participated in the Bulgarian national movement.
With the exception of a five-day independence in the winter of 1906, when a peasant uprising declared the autonomous Republic of Komrat, the Gagauzian people have mainly been ruled by the Russian Empire, Romania, the Soviet Union, and Moldova.
However the Gagauzes are characterized by the highest proportion of the Near Eastern DNA lineages. This fact agrees with the historically documented information on the migration of the Gagauzes to the Southern Bessarabia from the territory of the Balkan Peninsula. Genetic findings testifies to the emergence of the Near Eastern lineages in the Gagauz paternal gene pool, probably, long before the penetration of the Seljuk Turks and the Ottoman Turks into the Balkans. The analysis of the genetic distances confirms this reasoning. In population comparisons the Gagauzes are more closely related genetically to the neighboring southeastern European groups, than to linguistic-related Anatolian populations. More considerable distinctions in the distribution of Y chromosome components appeared between the Gagauzes and the Turkic peoples from Central Asia. Besides, in virtue of the lack of social barriers between the local and the Turkic-Orthodox populations of the Balkan Peninsula the ongoing intensive reciprocal gene flow was accompanied by the gradual dissolution of the Asian genetic component in the pool of Balkan genes. In this case is proposed the multi-step process of language shift in accordance with the elite dominance model, i.e. Turkification.
In August 1990, Comrat declared itself an autonomous republic, but the Moldovan government annulled the declaration as unconstitutional. The Gagauz were also worried about the implications for them if Moldova reunited with Romania, as seemed increasingly likely. Support for the Soviet Union remained high, with a local referendum in March 1991 yielding an almost unanimous "yes" vote to stay in the USSR; Moldovans in Gagauzia, however, boycotted the referendum. Many Gagauz supported the Moscow coup attempt, further straining relations with Chişinău. However, when the Moldovan parliament voted on whether Moldova should become independent, six of the twelve Gagauz deputies voted in favor.
Gagauzia declared itself independent on 19th August 1991 – the day of the Moscow coup attempt – followed by Transnistria in September. Some believe that these moves prompted the nationalist Moldovan Popular Front to tone down its pro-Romanian line and speak up for the rights of minorities. In February 1994, President Mircea Snegur, opposed to Gaugauz independence, promised a Gaugauz autonomous region. Snegur also opposed the suggestion that Moldova become a federal state made up of three "republics": Moldova, Gagauzia, and Transnistria. This was the plan promoted by those wishing to rehabilitate the former Soviet Union. In 1994, the Moldovan parliament awarded "the people of Gagauzia" the right of "external self-determination" should the status of the country change. This means that in the event -and only in that event- that Moldova decided to join another country (by all accounts this is referred to Romania), the Gagauzians would be entitled to decide whether to remain or not a part of the new state by means of a self determination referendum
On December 23, 1994, the Moldovan parliament produced a peaceful resolution to the dispute by passing the "Law on the Special Legal Status of Gagauzia" (Gagauz Yeri). Gagauzia became a "national-territorial autonomous unit" with three official languages – Russian, Gagauz and Moldovan/Romanian – and the date is now a Gagauzian holiday. Many European human-rights organizations recognize Gagauzia as a successful model for resolving ethnic conflict.
As a result of a referendum to determine Gagauzia's borders, thirty settlements (three towns and twenty-seven villages) expressed their desire to be included in the Gagauz Autonomous Territorial Unit. In 1995, George Tabunshik was elected to serve as the Governor (Bashkan) of Gagauzia for a four year term, as were the deputies of the local parliament, "The People's Assembly" (Halk Topluşu) and its chairman Peter Pashali.