The Mediterranean freshwater fish biodiversity is in sharp decline, being threatened by several anthropogenic stressors. Among these, the introduction of non-native taxa plays an important negative role, clearly visible in the Northern Adriatic district, where endemic marble trout is heavily impacted by Atlantic brown trout via hybridisation and genetic introgression. In contrast to the situation in the Slovenian Soca River drainage, Northern Italian populations are probably all hybridised. Against this background, genetic screening is crucial in fisheries management actions, such as supportive breeding and stocking. Here, we underline the utility of genetic screening by presenting novel multilocus microsatellite data of Northern Italian marble trout populations. First, we unravel significant subpopulation structure even at the microgeographic level. Second, we point to complex scenarios of genetic introgression in the wild, where the reliable selection of suitable marble trout spawners necessitates from complete genetic control to avoid the propagation of hybridised specimens in the hatchery environment. Such a propagation would be particularly ominous when applying multiple generation captive breeding as evidenced by a realistic simulation case study. Finally, we outline a catalogue of best practice, implemented in fisheries management in South Tyrol since 2016.