Sequences from two DNA non-coding regions, the atpB/rbcL spacer region in the chloroplast genome and the internal transcribed spacer region of nuclear ribosomal DNA (ITS 1 and 2), are being used to resolve species relationships within Capsicum (chili peppers). Thirteen distinct species of Capsicum (including C. galapagoense ) are in our sampling as well as representatives of five cultivated varieties. Both Lycopersicon and Lycianthes are included as outgroups. The preliminary ITS sequences are subject to numerous insertion/deletions and two different copies are present in the species surveyed to date. Plasmid cloning with subsequent gel electrophoresis is being employed to separate the two ITS copies. The chloroplast spacer region exhibited no insertion/deletions. Both the ITS region and atpB/rbcL spacer region exhibit an appropriate level of variation for this study. Preliminary results with a reduced sampling indicate a strongly supported sister group relationship between C. eximium and C. annuum. Two different varieties of C. baccatum are resolved as sister taxa.

Key words: atpB/rbcL spacer, botany, Capsicum, ITS, Solanaceae, systematics