<p dir="ltr">Description of the data and file structure</p><p dir="ltr">We collected 2,034 <i>Lucilia cuprina dorsalis</i> individuals among 86 populations from sheep-grazing regions across the continent. Each fly was genetically characterised at 20,000 loci using DArTseq, a reduced complexity genome sequencing strategy.<b> </b></p><p dir="ltr">SNP genotypes, silicoDArT genotypes, and respective metadata of<i> Lucilia cuprina dorsalis</i> genotypes.The data file contains comprehensive genotypic information for 2034<i> Lucilia cuprina dorsalis</i>, including 26,277 SNP and 26,277 silicoDArT marker scores, corresponding marker sequences, and associated metadata. </p>