The advent of target capture loci for flagellate plants has been a game changer for fern systematics, allowing pteridologists to readily join the phylogenomics revolution by using hundreds of nuclear loci to infer divergent relationships at and below the level of family. However, the use of target capture loci to infer reticulate relationship within fern polyploid and hybrid complexes continues to be hampered by the bioinformatic complexities of reconstructing homeologous sequences from these biparentally inherited markers derived from short read data. Here we evaluate one approach, the recently published SORTER bioinformatic pipeline, for phasing and assembling homeologs for across multiple target capture loci to infer reticulate relationships using traditional phylogenetic methods. First, we demonstrate the effectiveness of SORTER for inferring the parentage of five allotetraploid species in the well-studied Polypodium vulgare reticulation complex.  Then, we address the advantages and limitations of SORTER for inferring the parentage of homoploid hybrids derived from divergent lineages within the species Polypodium pellucidum and for reconstructing homeologs and identifying the progenitors of the allopolyploid S. molesta within the poorly characterized genus Salvinia. We assert that SORTER is an excellent option for characterizing allopolyploid and homoploid hybrid diversity in various fern reticulation complexes, providing strong a phylogenetic foundation for broader inquiries into the frequency and factors promoting polyploidy and hybridization.