Reticulate evolution often leads to incongruence between nuclear and plastid phylogenies and comparisons between them have been used as a first approximation to disentangle patterns of hybridization. Because other processes like incomplete lineage sorting and phylogenetic error also produce similar incongruence patterns, additional sources of evidence must be incorporated. Here we focus on reconstructing the phylogeny of genus Lachemilla using nuclear ribosomal ITS and plastid trnL-F DNA sequences, and explore widespread patterns of cytonuclear discordance in this group. Lachemilla is a highly morphologically variable group of perennial herbs and shrubs, and a nearly ubiquitous member of the diverse Neotropical high-altitude grasslands. Our analyses identified four major clades within Lachemilla that are in part congruent with previous morphological classifications of the group. Furthermore, using multiple sources of evidence, including a procrustean approach to cophylogeny estimation, coalescent-based simulations, phylogenetic networks, chromosome counts, and genome size estimations, we also revealed a large-scale pattern of incongruence between the plastid and nuclear phylogenies in Lachemilla, which is mainly the result of widespread hybridization and polyploidy. We also estimated that the origin of Lachemilla in South America (~14.5 mya) predates the "rapid-uplift" diversification model that has been suggested for other high species-richness Andean plant clades, but following the formation of the high-elevation Andean grasslands during the last 5 mya, a rapid accumulation of particular nested lineages occurred has contributed to the ubiquitous presence of Lachemilla in these biomes.