Bradysia alpicola was collected from Cerov forest, Slovakia. Genomic DNA was extracted from an adult male fly using a protocol modified for low-input starting material, developed by C. Laumer at the Wellcome Sanger Institute (dx.doi.org/10.17504/protocols.io.bypypvpw). The samples were quantified and quality-checked with Qubit and Nanodrop (ThermoFisher) and sequenced for 150bp paired-end Illumina reads on the Novaseq 6000 platform. If using this data, note that one sample was split across three sequencing lanes, so all three files should be downloaded.