A 3.7 kilobase region of chloroplast DNA that includes atpB, rbcL, and their intergenic spacer was sequenced in 61 samples from 45 species of South American Lobeliaceae plus two outgroup samples from Australia. A clade of four hexaploid Lobelia species from Chile is sister to a clade comprising Lysipomia, Siphocampylus, Centropogon, and Burmeistera. Lysipomia is a monophyletic group of small cushion-forming plants endemic to the high Andes, and is sister to the clade comprising the remaining three shrubby genera, which are most diverse in the Andes, but also extend to Central America, Mexico, and the West Indies. Siphocampylus has capsular fruit and is inferred to be paraphyletic relative to fleshy-fruited Centropogon and Burmeistera, but fleshy fruits have evidently evolved repeatedly, making Centropogon polyphyletiC. Burmeistera is primarily bat-pollinated and monophyletic, having evolved from one group of species in Centropogon. The phylogenetic relationships within Burmeistera indicate that this genus underwent repeated episodes of rapid diversification when organismal diversification outpaced the accumulation of mutations in this region of chloroplast DNA.