Ixodes (Ixodes) mojavensis, n. sp. (Acari: Ixodidae), is described from all parasitic stages collected from the endangered vole Microtus californicus scirpensis Bailey, 1900 (Rodentia: Cricetidae), Mus musculus L. 1758 (Rodentia: Muridae), and Reithrodontomys megalotis (Baird; 1857) (Rodentia: Cricetidae) in the Amargosa Valley of California. When first collected in 2014, this tick was tentatively identified as Ixodes minor Neumann, 1902 because the nucleotide similarity between its 16S rDNA sequence and a homologous GenBank sequence from an I. minor from the eastern U.S. was 99.51%. Nevertheless, adults of I. mojavensis differ morphologically from I. minor by hypostomal dentition, absence of a spur on palpal segment I, and punctation patterns; nymphs by the shapes of basis capituli, auriculae, cervical grooves and external files of hypostomal denticles; and larvae by the length of idiosomal setae and hypostomal dentition. DNA sequencing of fragments of 4 different genes, 12S rDNA, 16S rDNA, cytochrome c oxidase subunit I (COI), and intergenic transcribed spacer 2 (ITS2) of I. mojavensis and of closely related species of Ixodes shows that the mitochondrial gene sequences of the new tick species are almost identical to the I. minor homologous genes. Phylogenetically, the two species do not cluster in mutually exclusive monophyletic clades. However, ITS2 sequences of I. mojavensis and I. minor diverge deeply (≥ 5.74% maximum likelihood divergence) and are as different as homologous genes from other recognized species. The discrepancy between the two sets of genes is suggestive of past mitochondrial introgression or incomplete mitochondrial lineage sorting.