Mitochondrial genome is a part of the oxidative phosphorylation metabolic pathway and is responsible for the production of energy in an organism. Still, the impact of mitogenome inheritance on the production traits in livestock is rarely studied. Using NGS technology, 109 complete mitogenomes of Holstein cows were sequenced, representing 109 maternal lineages. Magellan software was used to assign mitogenome sequence information to 2.373 cows and to use their milk production records (milk yield, fat yield; and protein yield) for the first three lactation. Quantitative genetic model was used to estimate the proportion of total variance explained by cytoplasmatic (mitochondrial) inheritance (m2). m2 was estimated with four different models; i) cytoplasmic model with maternal lineages (CITO-MODEL), ii) haplotypic model with mitogenome haplotypes (HAPLO-MODEL) iii) amino-acid model with unique amino-acid haplotype combinations (AMINO-MODEL) and iiii) model with evolutionary haplogroups (EVOL-MODEL). Cytoplasmatic (mitochondrial) inheritance, interaction herd-year-season, permanent environment and direct additive genetic effect were included in model as random effects. Age at first calving was used as covariate and was modeled as linear regression. Region (county) was included in model as fixed class effect. The estimated proportions of the phenotypic variances for the first three lactations, explained by m2rod, m2hap and m2aminohap were ranging from 7% to 10% for the milk yield. For the fat yield, the estimated proportions of the phenotypic variances for the first three lactations, explained by m2rod and m2hap, were ranging from 5% to 8%. The highest proportions of the phenotypic variance for the first three lactations, explained by m2rod, m2hap and m2aminohap, were for the protein yield, ranging from 8% to 15%. The estimated proportions of phenotypic variances in the CITO, HAPLO and AMINO models were significant for all three milk production traits. No significant component of variance attributable to the evolution haplogroups was found for the milk production traits. The phylogenetic analysis of Holstein mitogenomes revealed a large variety of haplotypes within the T3 haplogroup that is specific to most Bos taurus breeds in Europe. The presence of a smaller number of Holstein cows within haplogroups T2 and T5 indicates the possibility of crossbreeding between autochthonous cow breeds with Holstein bulls. The performed analyses and the obtained results showed that a considerable proportion of the phenotypic variance in milk traits was explained by the mitogenome variation. This contributes to the knowledge of the genetic architecture of milk production traits that are the basis for a further improvement of breeding values in cattle. The utilization of mitogenome inheritance in practical animal breeding remains challenging.