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Genetic diversity and phylogenetic relationship of three Croatian autochthonous cattle breeds was analyzed using a sequence of the mtDNA D-loop region. Among Busha, Istrian, and Slavonian Syrmian Podolian cattle 146 unrelated animals were tested. The sequencing of 780 base pairs of the mtDNA D-loop region revealed 39 polymorphic sites representing 28 different haplotypes. The highest numbers of haplo - types were observed in the Busha population and the lowest in the population of Slavonian Syrmian Podolian cattle, while the highest level of sequence diversity within a population was observed in the Istrian cattle. Our results indicate a high level of mtDNA diversity in the populations of Busha and Istrian cattle and a low level of preserved diversity in the population of Slavonian Syrmian Podolian cattle. The sequence analysis showed substantial subdivision between the breeds ( F ST = 0.1434), and a large fraction of variation within the breeds. Although the dominant haplotypes are classified as the T3 haplogroup, some of the haplotypes are classified as the rarer T2 and T5 haplogroups. Genetic information based on mtDNA typing has a great importance for the future conservation management and preservation of genetic diversity in autochthonous cattle breeds.

Genetic variation in three Croatian coldblood horse populations was analysed using a sequence analysis of the proximal part (nt 15 498-15 821) of the D-loop region of mtDNA. Twenty unrelated horses were chosen from the Posavina horse and the Croatian Coldblood breeds and fifteen horses from the Murinsulaner horse population. Sequencing of the proximal part of the mtDNA D-loop region revealed 26 polymorphic sites representing thirty haplotypes which were clustered into eight haplogroups. A wide variety of mitochondrial haplotypes of the analysed horse breeds were clustered into eight different haplogroups. Two haplogroups (D and F) were specific to Posavina horse, five haplogroups were shared among the Croatian Coldblood and Murinsulaner horse, the fact that can be explained by selection strategy at the beginning of the 20 th century and possible gene flow between the two populations. These results indicate the presence of many ancient maternal lineages with high diversity in mtDNA. The genetic information based on mtDNA typing has a great importance for the future breed conservation strategy, especially for the critically endangered breed such as Murinsulaner horse.