The introduction of fish for stoking purpose is a common operation to manage fisheries. This may cause ecological and sanitary risks to native aquatic biodiversity especially in fishless Alpine lakes. In these ecosystems, fish have been introduced by anglers for ages. Europe imposes strictly controls on aquaculture facilities that breed fish for stoking purpose only for viral disease but not for bacterial or parasitic ones. Moreover, the role of alien fish as carriers of pathogens is poorly studied. For these reasons, we performed two fish sampling campaigns in two Italian Alpine lakes (Dimon Lake and Balma Lake) to have qualitative information about alien fish populations and to perform a bacteriological survey on captured fish. In Dimon Lake we captured individuals of Cottus gobio and of Phoxinus phoxinus, while only individuals of Salvelinus fontinalis were sampled in Balma Lake. We isolated Aeromonas sobria and Plesiomonas shigelloides in Dimon Lake, which are bacteria widespread in aquatic environment. In Balma Lake, one fish was positive for Yersinia ruckeri, a primary pathogen present in aquaculture facilities that reared salmonids. Our study show how alien species may introduce bacteria that could be more virulent for native aquatic fauna or even pathogenic bacteria.