The Genomics for Australian (GAP) Phylogenomics has the ambitious long-term goal of resolving the Australian Angiosperm Tree of Life (AAToL) to species level using a common set of hundreds of predominantly nuclear molecular markers. Data captured from the universal target enrichment bait set Angiosperms353 (Johnson et al. 2019 doi:10.1093/sysbio/syy086) are released here. For selected datasets, data captured with alternative probe sets in addition to the Angiosperms353 bait set are also released here.