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.