Chamomile (Anthemis sp) is an important medicinal plant in the world that is widely used today. In order to investigate the proxidase diversity of three species of Anthemis (A. pseudocotula, A. haussknechtti and A. triumfetti) nine population were studied. From eleven abserved- alleles, there were three rare alleles in A triumfetti species. Four private alleles were seen in A. pseudocutula and A. triumfetti species (in PXA and PXB locus). The higher and lower genetic distance were obtained between A. pseudocutula and A. triumfett and between A. triumfetti and haussknechtti respectively. Using principal components analysis. result showed that the A. psudocutula had the most distance from other species and cluster analysis was performed in a separate cluster. There was no correlation between ecological data and genetic character but correlation between latitude and longitude with genetic characters was significant at the 1% level. Analysis of molecular variance among populations was 18% and within of the population each species was 44%.