Cruckshanksia Hook. & Arn. and Oreopolus Schltdl. Rubiaceae (Rubioideae – Coussareeae), endemic genera of Chile and Andean Argentina, have historically been highly taxonomically unstable. Molecular analyses have confirmed Oreopolus as the sister group of Cruckshanksia; however, the relationships among its species are still not resolved because previous studies have not considered all species of the genus and the published topologies have many unsupported nodes. For this reason, we carried out a phylogenetic study with all the species currently recognized by recent revisions, using two nuclear DNA regions and five plastid regions, to elucidate the relationships between species. In addition, the evolutionary history of the group was estimated based on divergence times, and a character reconstruction was performed. The results corroborate that Oreopolus is the sister group of Cruckshanksia. Cruckshanksia is monophyletic and composed of two principal clades. Clade I is composed of Subclade I (C. pumila and C. verticillata) associated with C. montiana; Clade II is composed of Subclade II (C. palmae and C. macrantha) and Subclade III (C. lithiophila and C. hymenodon). With 81% probability the common ancestor of the genus Cruckshanksia had petaloid appendices associated with two independent lines of evolution. The probability that the common ancestor of the Oreopolus‒Cruckshanksia clade had equal calyx lobes is 50%.