In the Republic of Croatia, genetic variability of wild rabbits (Oryctolagus cuniculus) has been previously analyzed only on the basis of the control region of mitogenomes in recent individuals. In this work, for the first time, an analysis of whole mitogenomes of wild rabbits is presented. The set of modern and historical mitogenomes consists of 44 fasta sequences, while in the analysis of the control region, the existing set was expanded to 123 fasta sequences. Bioinformatics tools such as (MEGA 7.0, PopArt and DNAsp) were used to approach the analysis of the above sets. The calculated p-differences between the mitogenome group and their control region indicate a very small nucleotide difference, with the exception of the group of individuals from southern Spain, which showed a clear separation of A and B mitochondrial lineages in a later analysis, with individuals from Croatia clearly assigned to the B lineage. In total, 44 individuals yielded 15 haplotypes, whereas 123 individuals yielded 11 haplotypes. Phylogenetic trees and networks (Maximum Likelihood Tree, Neigbor Joining Tree and Median Joining Network) were successfully constructed to demonstrate the importance and significance of mitogenomes in relation to other scientific research in the field.