Cyanogenesis, the release of toxic cyanide from living cells, plays an important role in the defence system of certain plant (e.g. Fabaceae) and animal (e.g. Zygaenidae) taxa. The larvae of a significant number of Zygaena moth species (Zygaenidae) preferentially feed on cyanogenic Fabaceae and some of them are able to sequester cyanogenic compounds of their host plants. Using secondary structure variation of the small-subunit rRNA, we tested the currently accepted evolutionary hypothesis explaining species diversification in the genus Zygaena. We derived secondary structures considering evidence from covariation patterns and thermodynamic folding and applied structural information in a phylogenetic analysis. Contrary to previous assumptions, our results suggest that the use of cyanogenic larval host plants is an ancient trait and that the ability to feed on cyanogenic plants was probably already present in the most recent common ancestor of Zygaena. The utilization of acyanogenic plants in Zygaena species appears to be the result of a single secondary, reverse, larval host-plant shift. (c) 2006 The Linnean Society of London.