Phycella (Amaryllidaceae) is a clade of lilies endemic to the Mediterranean-type ecosystem of Chile. To approach the evolutionary history of Phycella, we sampled a total of 137 individuals from 47 populations, including all described taxa throughout the geographic range of the group, and sampled 893 nuclear genes (1135 exons) through hybrid capture. These data largely resolved the phylogeny of Phycella with high support and demonstrated substantial phylogenetic resolution at the population level. Near-complete plastomes were extracted from raw reads and assembled for all samples to compare with the nuclear framework and examine complex evolutionary processes. Using phylogenetic network and modeling approaches, we identified major cytonuclear discord, attributable to proximity-based gene flow among recently diverged species through the speciation process, largely involving cytoplasmic DNA. Analyses of niche overlap among species and nuclear clades suggest that the diversification of Phycella was associated with niche divergence, supporting a predominantly geographic mode of speciation in the group, likely driven by the mountainous landscape characteristic of diversity and endemism center of this clade in central Chile. The combination of high-resolution molecular data Finally, we present a major integrative taxonomic proposal that divides Phycella into 18 species on the basis of molecular, morphological, and ecological data. Overall, our findings highlight the value of strong sampling of both populations/individuals and genetic loci for speciation studies, which in combination with morphological and ecological data was key to identifying both evolutionary processes and a confident taxonomic framework for contextualizing these processes.