The nuclear ribosomal ITS region and the chloroplast trnL-trnF (trnLF) intergenic region were sequenced for 45 accessions of Paranephelius and six accessions of Pseudonoseris, the two genera of the subtribe Paranepheliinae (Liabeae, Asteraceae) distributed in the alpine regions of the Andes. This data set was used to estimate relationships between these genera and within each genus to aid in evaluating morphological variation and classification. Our results with both ITS and trnLF markers support the monophyly of subtribe Paranepheliinae, and place Pseudonoseris discolor as the first diverged taxon sister to the clade containing Paranephelius. Pseudonoseris szyszylowiczii exhibited intraspecific divergence supporting intergeneric hybridization between Pseudonoseris and Paranephelius. Within Paranephelius, genetic divergence is low and not adequate to fully resolve phylogenetic relationships at the species level, but two genetically and morphologically recognizable groups were revealed by the ITS data. Several accessions possessing multiple ITS sequences represent putative hybrids between the two groups. These putative hybrids have caused some taxonomic confusion and difficulties in establishing species boundaries in Paranephelius. The divergence time estimates based on ITS sequences indicated that the stem of subtribe Paranepheliinae dates to 13 million years ago, but the diversification of the crown clade of the extant members began in the early Pleistocene or late Pliocene, perhaps associated with the uplift of the Andes and the climatic changes of global cooling.