Pediculus humanus capitis is a major obligate and district ecto-parasite of human which is distributed in different parts of the world and is under several research projects for population management and molecular analysis. In this study, one hundred and seventy head lice were collected from school girls at different high schools in five cities in south east of Tehran Province (Iran). They were analyzed using molecular methods for genotyping lice, Cytochrome Oxidase I (COI), for the first time in Iran. The phylogenetic analysis of the concentrated sequences of the head lice populations showed high divergence among the population collected from different cities. However, samples belonged to each city showed high homology with some of the GenBank sequences.