Mitogenomes are valuable data sources for phylogeographic and evolutionary studies of relatively closely related organisms. Here we describe eight complete sequences of moose mitogenomes belonging to the three clades of the European lineage and compare them with those of the Asian lineage. Mitochondrial genomes of moose and other cervids were used to infer highly resolved phylogenetic relationships and estimate divergence times. The analyses clearly distinguished two mtDNA lineages of moose and supported the division of the European lineage into three clades: East, West, and Central. The divergence of the European and Asian mtDNA lineages occurred in the Middle Pleistocene (ca. 443 kya), which significantly exceeds the fossil records of modern Alces alces dated to 100 – 200 kya. It indicates that the evolutionary history of the moose is more complex and could encompass inheritance of the ancestral variation. Our estimates also showed rapid diversification of present-day clades of the European lineage, which coincided with the transition from the Penultimate Glacial Period (MIS 6) and the Eemian interglacial (MIS 5) approximately 100 kya. Despite the strong division of the nucleotide sequences, we detected no evidence for the divergence of amino acid sequences between Clade Central and Clade East. The recent diversification of A. alces clades, in combination with their evident reciprocal monophyly, could be a result of low effective population size over its evolutionary history, augmented by severe bottlenecks during the Last Glacial Period. Our results are in agreement with the presence of different glacial refugia recently proposed for three identified clades of the European lineage and suggested the relict character of the Scandinavian (from Clade West) and the Biebrza moose population in northeastern Poland (belonging to Clade Central).