Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species‐rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction‐site‐associated DNA sequencing data. We assessed the congruence of topologies generated from...