Abstract The cyst nematode, Globodera pallida, is a major pest of potato, a plant native to South America. To investigate its phylogeography, an extensive sampling survey was conducted in 2002 in Peru and has laid the foundations of the ancient evolutionary history of this nematode species. We argue that the uplift of the Andes Mountains has triggered a variety of adaptive biotic radiations for Solanaceous plant-parasitic nematodes and has represented a key factor for the evolution and specialisation of Globodera species. We discuss the consequences of the wide genetic diversity observed in South American populations on the efficiency and durability of potato resistance and also the reliability of current molecular identification tools for quarantine purposes. Finally, we emphasise the need to get a more in-depth taxonomic characterisation of some of these nematode populations, and to conduct more extensive sampling in South America, especially south of Lake Titicaca, in order to understand fully potato cyst nematode evolution and their adaptation to their host plants.