The intron of the chloroplast gene rpl2 is absent from relatively few lineages of angiosperms, and is thus potentially a useful phylogenetic character. A previous extensive survey of Leguminosae showed that the intron was missing from chloroplast genomes of one of the two species sampled from the large caesalpinioid genus Bauhinia. A survey of 78 species of this genus, representing all four subgenera and most of the currently recognized sections, shows that the intron is absent from numerous species of the genus, in a pattern that is correlated, albeit imperfectly, with taxonomic groupings. The intron is present in chloroplast genomes of two of three species sampled from the small subg. Elayuna, all but one species of subg. Phanera, and the monotypic subg. Barklya. In contrast, the intron appears to be absent from the gene in nearly all species of subg. Bauhinia. Three species in two sections of subg. Bauhinia were found to be polymorphic for the presence of the intron. Comparisons of the distribution of the intron with current taxonomic groupings and the topology of a recent morphological cladistic analysis suggest either that there may have been multiple independent losses of the intron in the genus or that a polymorphism has been retained across speciation events.