While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages—clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord.