Analysing the entire mitogenome provides insights into the genetic diversity, evolution and phylogeography of the different goat breeds and their wild relatives. The meta-analysis of 564 goat and 5 sheep mitogenome sequences also included nine mitogenomes of Croatian goat breeds mapped from whole genomes using the Galaxy platform bioinformatics tools, with an average length of coverage of 100% and an average depth of coverage of 1630.62. The BEAST analysis revealed the presence of haplogroups A, B, C, D, F and G, with the a posteriori value of 1 indicating a significant separation of haplogroups, but also revealing two unknown groups of Asian origin. The time of divergence was estimated between all pairs of haplogroups, while the divergence between sheep and goats was estimated at 833892 years ago. In the Middle East region, all haplogroups were detected, while the Croatian goats belonged only to haplogroup A. The study included 110 ancient sequences of goats, which showed a more even representation of haplogroups compared to modern goats, although haplogroup A remained dominant and most widespread across Eurasia. The MJ network clearly separated the aforementioned haplogroups, confirmed the evolutionary relationships and showed the genetic similarity between the domestic goat and its relatives. The greatest diversity of haplotypes was found in the mtDNA D-loop region (Hd=0.9992), followed by the ND5 segment. This meta-analysis created a database of mitogenome sequences for future archaeogenetic analyses and for the development of mitogenome SNPs on the SNP chip panels for commercial use to analyse and monitor genetic diversity.