RADseq data of the Lake Malawi cichlid species Aulonocara koningsi, Labeotropheus trewavasae, Labidochromis caeruleus, and Metriaclima mbenjii, and of F2 individuals from two hybrid crosses, one between Metriaclima mbenjii and Aulonocara koningsi, and the other between Labidochromis caeruleus and Labeotropheus trewavasae. The crosses will be used to investigate the genetic basis of complex trait variation associated trophic evolution.