Abstract: Iranian Bactrian camels are in critically endangered status, while dromedary camels with stable population size are economically important in hot desert area regions. This pioneering study was conducted to observe the genetic diversity of Iranian camels using mitochondrial DNA. A fragment of 1657 bp from mitochondrial DNA including Cyt-b (1052bp) and D-loop (605 bp) was amplified. Eleven mtDNA haplotypes and three haplogroups were detected in120 individuals from four populations. Mitochondrial sequences showed extensive sharing of haplotypes across dromedary populations. For Bactrian camels, we identified 1 and 30 polymorphic sites in D-loop and Cyt-b respectively, while mentioned values were 51 and 58 for dromedaries.