Pectolinarin was isolated from the ethyl acetate fraction of Cirsium setidens using open column chromatography and was analyzed using spectrometry. Pectolinarin content in Cirsium spp. was determined using HPLC/UV. Pectolinarin content in the aerial part of Cirsium spp. was higher than that in the root and pappus. Pectolinarin content was highest in the aerial part of C. chlorolepis (110.65mg/g extract). Consequently, the aerial part of C. chlorolepis has potential for use in new natural medicinal products, health supplements, and beverages.