This protocol builds on Suchan et al. (2016). It has been modified to work on fresh and museum samples of birds, specifically tested on Regent Honeyeater (Anthochaera phrygia).The detailed protocol contains three main sections: (A) preparing ddRAD libraries as probes, (B) preparing whole genome libraries for samples of different quality, and (C) using probes to hybridise and isolate the same fragments from all samples.Start with up to 600 ng whole genomic DNA per sample (our minimum was 14 ng), resuspended in 8 μl. Always include a negative control (containing no DNA, just buffer) in parallel to samples.