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Cricetulus migratorius is widely distributed in the northwestern arid regions of China. Here, the complete mitochondrial genome (mitogenome) of C. migratorius is reported, to our knowledge, for the first time. It was found to be 16,246 by in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region, and showed characteristics typical of the vertebrate mitogenome. Comparative analyses of mitogenomes of Cricetulus species showed that hamster mitogenomes had the same arrangement and organizational structure. The base composition was AT-rich for all Cricetulus species. We elaborated the PCG sequence and found that the main differences in the start and stop codons were in the ND3 gene; the most frequently used co-dons were AUU (Ile) and CUA (Leu), and the AT-content at the 3rd position was lower than that at 1st and 2nd positions in all Cricetulus species. The second tRNAser had lost the dihydrouridine stem-loop structure, which is found in all Cricetulus species. We also elucidated the structure of the control region (the extended termination associated sequences, the central conserved sequences, and the conserved sequence blocics), and the putative origin of replication for the light strand in all Cricetulus species. Based on mitogenome data with four reconstructed methods, phylogenetic trees showed high resolution in the divergent clades within Cricetulus. The results indicated that Cricetulus kamensis is at basal position, and has the earliest split among all Cricetulus species. Cricetulus griseus and Cricetulus longicaudatus clustered in a subdade, and were separate from C. kamensis. As previous studies have shown, Tscherskia triton is part of Cricetulus with high support value. It is noteworthy that C. migratorius is a young species, and has a close relationship with Allocricetulus eversmanni within Cricetulus, which is closer to the subgenus Allocricetulus. (C) 2016 Elsevier B.V. All rights reserved.