The dreissenid quagga mussel, Dreissena rostriformis bugensis, is an invasive species native to the Black Sea region that has recently spread to Western Europe. This organism has recently colonized Swiss northern perialpine lakes, causing major changes to aquatic ecosystems and impacts on human activities. Due to its competitiveness, the quagga mussel takes advantage of human mediated transport to reach new environments. Therefore, the management of quagga mussel should seek to prevent further spread and minimize its negative impact. With this aim, the early detection by environmental DNA (eDNA) methods is increasingly applied in freshwater systems. Here, an approach based on species-specific primer targeting the quagga mussel from eDNA was applied to Lake Lugano and Lake Maggiore, two large perialpine lakes at risk of invasion due international tourism. Our results are the first to show that the quagga mussel has spread south of the Alps and suggest that in both the lakes the colonization is in the early stages. Additionally, they indicate that the eDNA approach is a powerful tool for the early detection of quagga mussel invasions, and may be applied to reduce the resulting ecological and economic impacts.