The Pueraria flowers, Puerariae Flos [Puerariae Lobatae Flos (the flowers of P. lobata) and Puerariae Thomsonii Flos (the flowers of P. thomsonii)], have been used as crude drugs to counteract the overconsumption of alcohol in Japan and China. Both types of Puerariae Flos contain a large amount of isoflavones and saponins. Simultaneous analysis of the total saponin and isoflavone fraction within the flowers has proven difficult thus far; however, profile analysis of saponin and isoflavone levels was attempted in this study by using HPLC coupled to an evaporative light scattering detector (ELSD). A characteristic peak of kakkalide was common in the chromatograms of extracts originating from the flowers of P. lobata, though original habitats were different. Tiny peaks of saponins were also observed in chromatograms of all specimens derived from P. lobata. In the chromatograms of six out of eight extracts of Puerariae Thomsonii Flos originating from Guangdong, China, characteristic twin peaks corresponding to tectorigenin 7-O-xylosylglucoside and tectoridin were observed. The distinctive twin peaks were not found in the chromatograms of the extracts produced in Hunan and Sichuan. Although the amounts of total saponins and isoflavones obtained from Puerariae Lobatae Flos were almost the same, those of Puerariae Thomsonii Flos varied remarkably and were not related to habitat. A good yield of a new isoflavone glycoside was obtained from some specimens of Puerariae Thomsonii Flos; the structure was determined to be 6-hydroxygenistein 6,7-di-O-glucoside.