These data were compiled to highlight hybridization mosaics and genotype-environment associations across three study systems containing taxa critical to widespread plant communities in western North America: Artemisia tridentata, Ericameria nauseosa, and Sphaeralcea fendleri. Objective(s) of our study were to: (1) use genomic data to identify divergent evolutionary lineages (hereafter parental taxa) and hybrids among them, (2) assess correlations between allele frequencies and environmental gradients that may be indicative of adaptation and use machine learning algorithms to predict ancestry based on the environment for each lineage (i.e., parental taxa and hybrids), and (3) leverage relationships between environmental characteristics and ancestry to project parental and hybrid climate envelopes across geographic space and quantify the ecological ramification of hybridization for each study system in both present and future climates. These data represent reduced representation genomic data for multiple populations and individuals across western North America for Artemisia tridentata, Ericameria nauseosa, and Sphaeralcea fendleri. These data were collected in or created for Artemisia tridentata and Ericameria nauseosa in 2017-2019 across the entirety of the range of these systems in western North America and for Sphaeralcea fendleri in 2022 in New Mexico, USA. These data were collected by the University of Nevada, Reno, US Forest Service (Rocky Mountain Research Station), Bureau of Land Management, and the U.S. Geological Survey. A couple leaves from a single plant were collected and identified in the field by experts. These data can be used in further landscape genetic studies within these systems in this region. Either can be subset to particular regions or added to projects.