Heliotrapium sect. Cochranea (Heliotropiaceae) consists of 19 species endemic to the coastal Atacama Desert of Chile and Peru. This section has one of the most restricted geographic distributions and is the largest among the South American sections of Heliotropium. We performed a phylogenetic analysis of a total of 92 species using nuclear ribosomal ITS and chloroplast ndhF, rpsl6, and trnL-trnF sequences, and estimated the divergence times of major lineages of the group. Our results suggest that Heliotropium sect. Cochranea is monophyletic. There are two main well-supported lineages within the section: one is H. pycnophyllum, which is sister to rest of the species in the section. Within this second lineage, H. filifolium, H. glutinosum, H. krauseanum, and a large polytomous group composed of 15 species form a tetratomy. The age estimates using the penalized likelihood method suggests a minimum age of 14.0 ± 2.0 My for section Cochranea, and 4.6 ± 0.9 My for the large polytomous group within it. Heliotropium sect. Cochranea may have originated in the Miocene during the major uplift of the Andes, and then radiated in the Pliocene in the Atacama Desert.