Polyploidy, the state of having more than two full genomic complements in the sporophytic generation, is ubiquitous across the plant tree of life, including being a major component of bryophyte, fern, and angiosperm diversity. Polyploidization is also an important process generating that diversity in its role as a mechanism of “instantaneous” speciation. Genomic approaches have revolutionized our ability to study many aspects of polyploid evolution. However, the phylogenetic study of polyploidy has lagged behind due to the combined challenges of data generation and analysis. Here we introduce recent methods that allow researchers to include polyploids in multilocus phylogenetic analyses, and to infer their full (typically reticulate) evolutionary histories, using next-generation and “third-gen” sequencing approaches. While these tools are beginning to be applied to better understand vascular plant evolution, even less is known about the phylogenetic history of bryophyte polyploids, or the role of polyploidy in bryophyte evolution more broadly. Nearly 20% of bryophyte species are estimated to contain at least two ploidy levels, and many more undescribed polyploid species are expected. The moss Syntrichia occurs worldwide in a variety of habitats, comprising about 90 species, many of which are reported to contain multiple cytotypes. In addition to polyploidization generating new Syntrichia species directly, it may play a role in altering sexual systems in these mosses. Most Syntrichia species are dioicous--they have separate male and female gametophytes, with the sexes determined by a UV system (individuals with a U chromosome are male and those with a V are female). However, monoicy (a single gametophyte produces both male and female sex organs) is also common in the genus. In this talk, we present a case study on Syntrichia polyploid phylogenetics using a target capture approach with de novo assembly of target loci, including assembly of each homeolog in polyploid individuals. We infer several polyploids within Syntrichia, including tetraploids and hexaploids within a single named species. Furthermore, we phase these homeologs across loci to infer a multi-locus reticulate for the genus . Finally, we estimate sexual system ancestral states and test for correlation between sexual system and allopolyploidization. This case study not only reveals a more thorough picture of Syntrichia’s evolutionary history, it also shows the power of “polyploid phylogenetics” and, generally, polyploidy-considerate approaches in studying plant evolution.