Relationships among the major subclades in the fern family Pteridaceae have proven difficult to resolve. Here, we examine the backbone of this large and heterogeneous lineage using both phylotranscriptomic methods and a more focused, curated approach. We find that Pteridoideae and Parkerioideae are together sister to the rest of Pteridaceae and that Cryptogrammoideae is sister to Vittarioideae plus Cheilanthoideae. We find independent support from our phylotranscriptomic analyses, published cytological data, and genomic distributions of substitutions per site for several whole-genome duplication (WGD) events within Pteridaceae, mainly in Vittarioideae and Cheilanthoideae. However, the various inference methods gave differing approximations for the placement of WGD events within each clade. This study demonstrates that phylotranscriptomic analyses, which employ large datasets at the cost of requiring simpler models and potentially a greater risk of systematic error, can be used in concert with more curated approaches to resolve deep phylogenetic relationships. It also provides an example of the difficulty of confidently inferring ancient WGD event placement, even when using multiple methods.