**Abstract**

This chapter deals with the study of extranuclear hereditary material and the possibilities of using it to maintain endangered animal breeds. The chapter characterizes mtDNA, presents its genes and their functions, while also emphasizing the hypervariable control region. It reports on the results of previous researches, referring to international publications. It sheds light on promising areas of mitogenomic research. It shows the maternal genetic background of local native varieties according to the results of the study of available country/geographical region. It deals with reasons for endangerment and the arguments for preservation of autochthonous breeds. In addition, it gives place to discuss some exciting professional concepts in rare breed preservation.

**Keywords:** mitogenome, sheep, genetic diversity, haplogroup, haplotype, breed preservation, maternal lineages, within-family selection
