Archaeological fish remains are an important source for reconstructing past aquatic ecosystems and ancient fishing strategies using aDNA techniques. Here, we focus on archaeological samples of European whitefish ( Coregonus spp.) from Switzerland covering different time periods. Coregonus bones and scales are commonly found in archaeological assemblages, but these elements lack species specific features and thus inhibit morphological species identification. Even today, fish taxonomy is confusing and numerous species and ecotypes are recognized, and even more probably existed in the past. By targeting short fragments of the mitochondrial d-loop in 48 morphologically identified Coregonus scales and vertebrae from 10 archaeological sites in Switzerland, endogenous d-loop sequences were found in 24 samples from one Neolithic, two Roman, and four Medieval sites. Two major mtDNA clades, C and N, known from contemporary European whitefish populations were detected, suggesting co-occurrence for at least 5000 years. In the future, NGS technologies may be used to explore Coregonus or other fish species and ecotype diversity in the past to elucidate the human impact on lacustrine/limnic environments.