The resource consists of genotype data (genetic constitution of an individual organism) for three freshwater macroinvertebrate species, Amphinemura sulcicollis, Isoperla grammatica and Baetis rhodani collected at sites in upland Wales during May 2012 and May 2013. New nucleotide tandem repeats in DNA sequences i.e. Novel microsatellites were developed for this project so that genetic analysis could be carried out within the three species. Extra data on how microsatellite scores were grouped i.e. binned into unique alleles is provided, to aid replication. The data was generated for Hannah Macdonald's PhD thesis: to study genetic structure and diversity, demographic species history and resilience in freshwater ecosystems. The work was carried out under Diversity in Upland Rivers for Ecosystem Service Sustainability (DURESS) project (Grant reference NERC NE/J014818/1). DURESS was funded by the Natural Environment Research Council (NERC) under the Biodiversity and Ecosystem Service Sustainability (BESS) programme. Full details about this dataset can be found at https://doi.org/10.5285/27da4400-9835-4241-9df9-a3b598f8d274
