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Simple Summary: By the 19th century, adequately producing, independent domestic animal breeds had developed in many regions around the globe. However, from the middle of the 20th century they have largely been replaced by high-performing, specialized, single-purpose cosmopolitan breeds. Breed maintenance is an activity aimed at rescuing old breeds from the threat of extinction. This process includes recording the valuable traits of a rare breed, specific diversity conservation selection, and utilization in the original production environment. Additionally, it deals with the history of breeds and the study of their genetic makeup. The aim of this paper is to evaluate the maternal genetic background of two autochthonous sheep breeds in Hungary. The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (KST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background. [ABSTRACT FROM AUTHOR]