Vector control measures, such as insecticides, have been game changers in reducing the burden of malaria throughout sub-Saharan Africa ever since widespread use begun in the 1950s. However, it is known from present-day genomic studies that insecticide resistance in Anopheles mosquitoes is on the rise, especially since insecticides are acting as a strong selective pressure leading to hybridization of closely related species. In this study we are interested in how population structures and genetic diversity observed today changed within the last century, which includes populations before, during and directly after the widespread use of insecticides. The majority of our samples will be pinned mosquito samples from museum or private collections. As DNA damage (fragmentation, base substitutions) accumulates after the death of an organism, we require different approaches to DNA extraction and library preparation than the ones used for present-day material in order to minimize the loss of informative short DNA molecules. Furthermore, we are aiming for a minimally destructive DNA extraction approach so the specimens can be returned to their respective collections after DNA extraction. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/