Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai‘i (the Big Island).