Phylogenetic analysis of plants has historically been hindered by the paucity of low- or single-copy nuclear markers available for amplification and sequencing. As a result, plastid markers dominated phylogenetic workflows due to their relative abundance and applicability across many taxa. However, as a consequence of their uniparental inheritance, plastid markers are unable to fully reflect the evolutionary history of individuals that have experienced recent hybridization, a defining feature of allopolyploids. Hybseq and the release of the GoFlag451 probe set represent a prime opportunity to augment existing phylogenetic knowledge through the inclusion of numerous single- to low-copy nuclear loci. Here we demonstrate the effectiveness of multi-locus hybseq data in inferring the phylogeny of a group with allopolyploids, with a pipeline incorporating recently available methods in polyploid read assembly (PATÉ) and locus phasing (homologizer), applied to the notholaenid ferns of Mexico and the US southwest. In addition to providing evidence of allopolyploid evolution within the clade, our well-supported multi-locus phylogeny provides a strong framework for a subsequent taxonomic treatment of Notholaena and its relatives.