The plant genus Saintpaulia (African violet) is endemic to a small area in northeastern Tanzania and has undergone a recent radiation producing species which are difficult to distinguish morphologically. Previous molecular work identified a group of eleven species of the ionantha complex that are indistinguishable using sequence analysis of the internal transcribed spacer (ITS) of the ribosomal DNA gene. Exon 2 of the chalcone synthase (CHS) gene was PCR amplified producing 21 sequences from Sa. ionantha and 11 sequences from four other Saintpaulia species. The genus Saintpaulia contains two CHS genes (SaCHSA and SaCHSD). SaCHSD was used to construct a gene tree of six species. The sequence analysis clearly distinguishes four of the five closely related species of the ionantha complex.