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Genetic relationships between wild boar populations in the southern regions of Iran still remain unclear. Therefore in the present study our aim was filling this gap and providing preliminary knowledge about the phylogenetic status of Iranian wild boar based on two datasets of the mtDNA control region (the 402-bp and 605-bp segments as the first and second datasets, respectively). Altogether 1063 and 490 sequences were used in the shorter and longer sequences, respectively (29 own samples and 1034 and 461 Genbank sequences from previous studies in the first and second datasets, respectively). Our findings revealed that the wild boars living in Southern Iran belong to the previously described three clades: Asian, Near Eastern 1 (NE1) and Near Eastern 2 (NE2) clades. The NE1 and NE2 clades sympatrically occupy a wide range across the southeast to southwest of Iran, whereas the Asian clade is restricted to a small area in the southeastern part of Iran. Our results propose the existence of a contact zone between the Near Eastern clades and the Asian clade in the studied area. The fixation index ( F ST ) and the analysis of molecular variance (AMOVA) demonstrated significant genetic structure among the identified clades. Some identified haplotypes have a wide distribution, which suggests that they are probably ancestral haplotypes or are likely to be a result of recent population expansion. Overall, current research demonstrates that Iranian wild boars have an important phylogenetic position among the others in the world. In other words, Iran is a very important region for addressing some of the topical questions about phylogenetic relationships among the Eurasian wild boar clades. [ABSTRACT FROM AUTHOR]