The distribution of the naphthoquinones ramentaceone and plumbagin was studied among 50 taxa of the genus Nepenthes. Naphthoquinone patterns support classifications based on homology of plastid and/or nuclear genes to some extent, with plumbagin predominant in sections Nepenthes, Urceolatae, Tentaculatae, and Regiae, ramentaceone predominant in sections Insignes and Villosae, and both isomers present without clear predominance in sections Pyrophytae and Montanae. Only 9 of 96 studied species contained both isomers in the same plant. Naphthoquinone data from artificial hybrids of known parentage allowed conclusions on the biosynthesis of these compounds and the heredity of the respective enzymatic steps.