Eurasian lynx ( Lynx lynx ) is one of the valuable felid Species in Iran which is distributed from North East to North West of the country and also in some parts of central Iran. Several factors including habitat destruction and degradation and the reduction of prey populations have impacted its population in Iran. Understanding taxonomic status of the current populations and the genetic diversity within the species are essential for a better conservation of this species. In the current study, phylogenetic relationships of Eurasian lynx in Iran were compared to other populations in the world and the genetic diversity of population was assessed. About 21 samples were collected across the country from which only 12 extracted DNAs were suitable for further genetic analyses. A fragment of 613 bp of D-loop gene was amplified and sequenced. Results of genetic diversity assessment showed a low nucleotide and haplotype diversity. A large proportion of the genetic variance was explained by variation within populations and the level of population differentiation based on F st values was moderate. Results of phylogenetic analyses demonstrated the presence of two Asiatic and European clades in Iran and genetic distance between them is about 0.012. The closest population to the Iranian lynx populations was the Caucasus population; therefore, Iranian lynx populations are most probably belonged to this suecies ( Lynx lynx dinniki ). Two haplotypes were identified within the sampled populations in Iran of which one was unique and only presented in Qazvin samples. Further morphometrics and ecological studies are required to shed light on the status of Qazvin population. Findings of the current study can be used in conservation and management of lynx populations in Iran.