"Long-Dan" and "Qin-Jiao" are two important TCM herbs since ancient times in China. In the Chinese Pharmacopoeia, the dried roots and rhizomes of four species from the genus Gentiana, e.g. Gentiana manshurica, G. scabra, G. triflora and G. rigescens, are recorded under the name of Gentianae Radix et Rhizoma ("Long-Dan" in Chinese), while the other four species from the same genus including G. macrophylla, G. crassicaulis, G. straminea and G. duhurica are recorded and used as the raw materials of Gentianae Macrophyllae Radix ("Qin-Jiao" in Chinese). On the basis of the establishment of a validated HPLC-UV method for quantifying simultaneously, five iridoid glycosides, e.g. loganic acid (1), swertiamarinin (2), gentiopicroside (3), sweroside (4) and 2'-(o,m-dihydroxybenzyl)sweroside (5) have been used successfully as chemical markers for the comparison of the species used as "Long-Dan", "Qin-Jiao" and their adulterants in the present study. The results suggested that four iridoid glycosides 1-4 commonly existed in both "Long-Dan" and "Qin-Jiao", while 2'-(o,m-dihydroxybenzyl)sweroside (5) also existed as one of the major components in "Dian-Long-Dan" species. Moreover, the contents of compounds 1-5 were various in different "Long-Dan" and "Qin-Jiao" species. Herein, we profiled and compared three "Long-Dan" species, four "Qin-Jiao" species and five adulterants by applying multivariate statistical techniques to their HPLC data sets to establish the differences and/or similarities.