High mountain lakes are mostly naturally fishless ecosystems that have received numerous trout introductions over the world. Extensive studies mostly developed in west North America have shown a large negative effect of these introductions on amphibians, although no extensive studies are available from other continents such as Europe. Fish were also introduced extensively in the Pyrenees (southern Europe), mainly trout for angling and minnows for their use as live bait for fishing trout. We studied the effect of non-native trout and minnows on the occurrence of amphibian species inhabiting Pyrenean lentic habitats. Chi-square tests and Generalized Additive Models were applied on a dataset of 12 environmental descriptors from 1739 water bodies surveyed from 2006 to 2016. After accounting for environmental characteristics we found a large negative effect of non-native trout and minnows on Pyrenean amphibians. Trout was negatively associated with four of the six studied species. Since minnows were only introduced in trout present lakes, they were only significant for Rana temporaria, the most distributed amphibian in the area. None of the palatable amphibians have been able to recolonise the lakes where minnow remain as the only fish species indicating a strong negative effect. Minnow is the non-native fish with a higher introduction rate in the mountain range indicating that it might be a threat for other species in the future. Therefore, the control of trout stocking and minnow release in high mountain lakes is necessary to preserve European and worldwide amphibian populations in these ecosystems.