In this research in order to survey genetic structure of Red Fox in central region of Iran, 32 sample tissues were collected from five Provinces (Isfahan, Tehran, Semnan, Kerman and Yazd). After DNA extracting, D-Loop gene of mitochondrial genome was amplified using polymerase chain reaction (PCR) and 327 base pairs (bp) of this gene were sequenced for each sample. The results showed that there are 24 different haplotypes in the samples and haplotype diversity is equal to 0.98. Based on the results of the analysis of molecular variance (AMOVA), there is an average similarity between populations and the highest amount of sample variance is related to inter population changes. Species expansion has not been occurred due to Harpending’s Raggedness index and its multi exponential diagram. However based on the results of Tajima’s D and Fu’s Fs statistics, it could be concluded that species expansion had been possible in the past but it was not significant. Phylogenetic tree shows that there is no independent genetic structure for studied populations and in population differences are greater than among population differences. Haplotype network curve has also confirmed this issue. Although it is not possible to adopt a protection strategy by studying a short part of species genome, but due to the results of this research it might be concluded that there is a good gene flow among populations and currently there is no evidence of bottle neck problem among Fox populations of these regions.