Ammi visnaga and Ammi majus are plants that have long been used in traditional medicine. Nowadays, both herbs are commercially marketed as alternative medicines in different formulations. The main active ingredients of A. visnaga are known as khellin and visnagin. Information on the quantitative amounts of both bioactive substances in the different organs of the plant is lacking. This study aims to determine the amounts of these two active substances in the five organs of both plants from Turkey and provide information to the pharmaceutical industry. For this purpose, a fast and reliable micellar electrokinetic chromatography method was applied. It was found that Ammi visnaga, flowers, seeds, and leaves are good sources of both khellin and visnagin. Ammi majus only contains khellin in its seeds and flowers.