Plague, a lethal zoonotic disease, primarily circulates within rodent populations and their fleas. In Iran, the widely distributed jird, Meriones persicus, serves as the principal reservoir for plague, with a belief in the existence of five out of its six recognized subspecies within the country. However, these subspecies are classified into four mitochondrial cytochrome b sub-lineages (IA, IB, IIA, IIB). This discrepancy, combined with the presence of an unnamed sub-lineage in central Iran awaiting taxonomic clarification, has left intraspecific taxonomy unsettled and obscured the true alignment between mtDNA sub-lineages and nominal subspecies. In this study, we investigated the intraspecific variation in the cytb gene across populations sampled throughout Iran, focusing on underexplored regions between the Zagros and Alborz Mountains and central Iran. While our genetic data generally support reported subspecies validity in Iran, we raise questions about M. p. baptistae, emphasizing the need for further data from its type territory in Pakistan. Two main lineages of M. persicus (I and II) exhibit geographical isolation, with limited overlap in the central Zagros Mts., where three subspecies (M. p. ambrosius, M. p. rossicus, and M. p. persicus) coexist. Superimposing infected rodents' geographic coordinates onto updated sub-lineages' distribution revealed a potential association between sub-lineage IA (M. p. rossicus) and all enzootic plague cases from 1946 to 2023. M. persicus rossicus extends into the Caucasus (where plague infections are common), Eastern Turkey, and Iraq. Consequently, interpreting this finding in the context of plague surveillance in Iran and neighboring areas requires caution.