Cattle breeding is one of the most important branches of animal husbandry in the whole world. With the domestication of cattle, the nomadic way of life began, and it developed more and more into the life we know today. As such cattle were the main source of skin, meat, and milk. While the use of SNP chips in cattle breeding is widespread and there are many commercial SNP chips of different densities, bovine SNP mitogenomic information from existing chips is not widely used so far as no successful validation of SNP mitogenome has been performed. In collaboration with NEOGEN Genomics, we selected 331 SNP mitogenomes to be included in the GGP100K (GeneSeek Genomic Profiler) SNP chip. Selection of SNP mitogenomes was based on variability in 16333 complete mitogenomic sequences from more than 150 breeds. In this study, we will describe the already mentioned selection and validation process of 331 mitogenomes involved in the GGP100K SNP chip. The aim of the study is to classify all haplogroups present, to quickly identify rare haplogroups (such as P, R, Q and T5) and to show the diversity of haplotypes. The obtained genotypes were compared and validated with the whole mitogenomic sequence, and no deviations were found. We also used phylogenetic analyzes and the development of a phylogenetic tree and network (Neighbor Joining Tree and Median Joining Network) to demonstrate the usefulness and informativeness of mitogenomic SNPs.