This study compared the antimicrobial activity and chemical composition of two plants used as "Injin" (Korean herbal medicine), namely, Injinho (Artemisia capillaris Thunberg) and Haninjin (Artemisia iwayomogi Kitamura). The ethyl acetate and ether fractions of crude methanol extracts from A. capillaris and A. iwayomogi were tested against three grampositive bacteria (Bacillus cereus, Bacillus subtilis, Staphylococcus aureus), two gram-negative bacteria (Escherichia coli, Pseudomonas fluorescens), and a yeast (Saccharomyceus cerevisiae). The antimicrobial activity of the ethyl acetate and ether fraction of both plants was strong, but that of A. iwayomogi extracts was higher than that of A. capillaris extract for the microbes tested. The minimum inhibitory concentration of the ether and ethyl acetate fraction of A. iwayomogi was highest for P. fluorescens and lowest for S. aureus and E. coli. We analyzed the chemical composition of the ethyl acetate fraction of A. capillaris and A. iwayomogi using gas chromatography-mass spectrometry. The main components of A. capillaris and A. iwayomogi were escoparone (86.82%) and scopoletin (20.47%), respectively.