We developed a probe set that captures exonic regions of 46 genes representing the phototransduction cascade and other light responses. We successfully capture an average of 64 percent of our targeted exome in 46 species across 14 orders. For a subset of species, we directly compare gene capture between our probe set and low-coverage whole genome sequencing. This BioProject contains Illumina reads of both captured vision gene sequence, as well as the shotgun whole genome sequences. Reference: White et al. 2021, A Novel Exome Probe Set Captures Phototransduction Genes Across Birds (Aves), Enabling Efficient Analysis of Vision Evolution. Accepted at Molecular Ecology Resources August 2021.