Rapid management responses against invasive species soon after their establishment are the most efficient way to limit their biological and economic impacts. Early detection and reliable monitoring is however challenging when cryptic taxa are involved. Here we show how environmental DNA (eDNA) metabarcoding of water samples efficiently unveiled an emerging invasion of Italian crested newts (Triturus carnifex), one of the most successful amphibian invaders in Europe. We compared and validated an eDNA survey by multilocus population genetics of wild‐caught individuals. Both approaches consistently mapped a localized T. carnifex invasion in northwestern Switzerland, most likely following imports from the Italian Po Plain. We found evidence of gene flow with the indigenous and endangered Triturus cristatus in nearby populations, suggesting a potential expansion. Yet the currently small invasive range should be efficiently contained by future eradication programs. This textbook case emphasizes the implementation of eDNA metabarcoding to screen aquatic communities for exotic species, from which targeted studies can be designed on emerging biological invasions.