Background: Mitochondrial DNA (mtDNA) variations are often associated with bioenergetics, disease, and speciation and can be used to track the history of women. Although advances in massively parallel sequencing (MPS) technology have greatly promoted our understanding of the population’s history (especially genome-wide data and whole Y chromosome sequencing), the whole mtDNA sequence of many important groups has not been fully studied. In this study, we employed whole mtDNA genomes of 209 healthy and unrelated individuals from the Daur group, a Mongolic-speaking representative population of the indigenous groups in the Heilongjiang River basin (also known as the Amur River basin). Results: The dataset presented 127 distinct mtDNA haplotypes, resulting in a haplotype diversity of 0.9933. The majority of haplotypes were assigned to eastern Eurasian-specific lineages, such as D4 (19.62%), B4 (9.09%), D5 (7.66%) and M7 (4.78%). We collected whole mitochondrial genomes from the 1000 Genomes Project, the Human Genome Diversity Project and published papers for population comparisons and phylogenetic analysis, and the results showed that the Daurians do have certain connections with the ancient populations in the Heilongjiang River basin but the matrilineal genetic composition of the Daur group was also greatly influenced by other non-Mongolic groups from neighboring areas. Conclusions: Collectively, the whole mtDNA data generated in the present study will augment the existing mtDNA database and deepen our understanding of the history of the Daurians as well as other populations from northern East Asia.