In this project, we provide whole genome data for the Daphnia longispina complex inhabiting large ponds and lakes in central and northern Europe. We generated reference data for the three species D. galeata, D. cucullata and D. longispina sequenced from clonal lines and whole genomes from four natural populations sequenced from single resting eggs using whole genome amplification. This dataset will provide insight into the intra- and interspecific genetic variability in the complex and the dynamics of introgression.