Genomic tools like RAD-sequencing can provide the resolution to understand the complex genetic patterns underlying cryptic biological invasions. Here we use this method to clarify the genetic consequences of a rampant invasion by the Italian pool frog (Pelophylax bergeri) north of the Alps, threatening the native P. lessonae and its hybridogenetic hybrid P. esculentus. Patterns of genetic structure were consistent with massive genetic introgression, except for an isolated mountain valley in Switzerland (Joux). Moreover, alien alleles also reached the hybridogens, which should be considered non-native as well. Potentially initiated during antic times, this hybrid swarm likely extends all over W-Europe and rises among the largest amphibian invasions documented on the old continent. Invasion genomics thus hold great promises to reliably inform conservationists, especially in animal groups for which conventional genetic markers may not always be diagnostic between closely-related, morphologically similar species.