To establish an microscopic method to identify two species of conventional chamomiles in Xinjiang.Methods:Using chloral hydrate and permeabilized powder method, and a digital microscope to observe the main microscopic characteristics of two species of chamomiles.Results:Both species of chamomiles have small calcium oxalate crystal clusters, glandular hairs, catheter, and so on. But their non-glandular hairs and pollen grains have obvious difference. Roman chamomile has non-glandular hairs and 3 apertures. The chamomile has no non-glandular hairs and 4 apertures.Conclusion:The differences of aperture on pollen grain and with or without non-glandular hairs can be used as new criteria to distinguish the two kinds of chamomiles. It will provide a scientific basis for the medicinal materials quality standards in further research and development.