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The heads of Artemisia capillaris have been used for medicinal purposes, as their choleretic effect of capillarisin (CAP) and 6,7-dimethylesculetin (DME) are known. However, hybrid plants between A. capillaris and A. japonica are often found in the crude drugs sold in the Japanese market, therefore observation of flowering dates, the ten morphological characteristics of flower heads, and CAP and DME contents, as well as RAPD (Random Amplified Polymorphic DNA) analysis were carried out for A. capillaris, A. japonica and their natural hybrid plants grown in the flood plain of the Sho-river, Takaoka, Toyama, Japan. Further, the pharmaceutical status of flower heads derived from the hybrid plants was discussed. The results showed that hybrid plants were similar to A. japonica, and when flower heads from the hybrid plants were mixed in crude drugs, the quality of the crude drug could decline because of traces of CAP and DME. Flower heads of hybrid plants could be detected with certainly by the presence of secretory sacs on corolla lobes of disk flowers and lower content of CAP and DME and removed.