Four mitochondrial genomes of Triticum species were sequenced and annotated: 1) (lo) durum mitochondrial genome, which is an alloplasmic line with Triticum longissimum(SS) cytoplasm and T. turgidum (AABB) nucleus, 2) T. longissimum, 3) T. turgidum and 4) T. tauschii (DD). Comparison showed major differences in atp6, nad9, nad6, rps19-p, cob and cox2 genes among all four species. Additionally, species-specific ORFs were also identified. A single nucleotide polymorphism search within known genes showed that the alloplasmic line differs from the two parental lines by six nucleotides in the cox3, mttB, rps2, rps4 and rps13 genes. We were able to recognize mitochondrial heteroplasmy based on single nucleotide variation (SNV) and regions of high SNV density within a given species. Structural differences between T. turgidum, (lo) durum and T. longissimum mitochondrial genomes were observed; however, conserved gene blocks and gene pairs among these species were identified. Three possible recombination events in gene blocks I, V and VI were recognized. We observed differences in the alloplasmic line, compared to its parental lines in: sequence, predicted genes, single nucleotide polymorphism (SNP) and genome structure. These facts support the hypothesis of the accelerated evolution of the mitochondrial genome when transferred into alien nuclear background. We also found that major gene changes recognized here appear to be common among Triticum species. Based on sequence assembly, we report full mitochondrial sequence of T. turgidum. We recognized 40 SNP differences compared to the T. aestivum mitochondrial genome, where 5 SNPs were found in known mitochondrial genes: rps1, rps2, cox3 and ccmFN. The T. longissimum and T. tauschii share highly similar genomes in structure and content, different only at the level of SNVs. A method to establish phylogenetic relationships based on mitochondrial genome sequence is proposed using differences in reference assembly with a common mitochondrial backbone sequence. We confirm conservation of the mitochondrial gene content within Triticum species. These results create background to explore the role of mitochondrial genes in conditioning nuclear cytoplasmic incompatibility in a wide range of Triticum alloplasmic lines and also deepen our understanding of evolutionary relationships that exist in the Triticum genus.