Chamomile serves as one of the most important medicinal plants. The most known secondary metabolites in chamomile species are volatile oils of triponoides, poly stilens, flavonoids and phenolic cafeic acid (Krori). These metabolites have wide variety of applications thanks to having medicinal properties of anti-inflammation, antispasmodic and bactericide activity. Also it is used to cure liver disorders and icterus (Zargari). Isozyme has been used successfully as biochemical markers n specific genetic and plant breeding areas. Isozymes serve as different molecular form of enzyme with protein nature, accelerating the same reactions. These molecules appear on electrophorese through pigmented reaction associated into enzyme function. They are products of different alleles located at locus or loci. The present research was conducted to evaluate genetic variation of thirteen chamomile populations and peroxidase enzyme quality. Peroxidase was extracted from fresh leaves and young seedlings. The PAGE approach was used to evaluations. There were three action sites on polyacrylamide gels called PX-A, PX-B and PX-C. based on results of electrophoreses on peroxidase enzyme, the most and least genetic distances were observed between populations Ghazvain-Ts2, Naghadeh-AT1 and Ghazvin-TS2,Ardabil2 respectively.