One of the causes of the decline in distribution and abundance of the endangered white-clawed crayfish Austropotamobius pallipes complex throughout Europe is the invasion of alien crayfish, and the associated spread of infectious diseases, primarily the crayfish plague caused by Aphanomyces astaci. Another relevant disease is microsporidiosis (porcelain disease), caused by Astathelohania contejeani and Nosema austropotamobii. Between 2021 and 2024, we conducted a monitoring survey, aimed at mapping the distribution of A. astaci, A. contejeani and N. austropotamobii in wild populations of A. pallipes and in two non-indigenous species in Trentino (North-East Italy). We applied a non-invasive sampling method (cuticular swabs) in 33 populations of A. pallipes, 2 populations of Procambarus clarkii and 4 populations of Faxonius limosus, to investigate the presence of A. astaci. Aphanomyces astaci was detected in eight thriving populations of A. pallipes, and the presence of a low virulence genotype (genotype group A) was confirmed in one of them. Aphanomyces astaci was detected in one of the two populations of P. clarkii, as well as in one of the four populations of F. limosus. No mortality outbreaks in populations of A. pallipes were recorded in Trentino during the study period. Specimens with macroscopic signs of porcelain disease were found in thirteen populations of A. pallipes, abdominal muscle tissues were collected and subjected to molecular evaluation; microsporidiosis was detected in all the tested crayfish: seven populations were infected only by A. contejeani, and in six populations both microsporidia were detected. Crayfish from one population of P. clarkii and one of F. limosus were tested for microsporidiosis as well, but the results were negative. Based on the presence of chronically infected but thriving populations across the Trentino territory, we provide suggestions for the management of A. pallipes populations in conservation actions which require the movement of specimens (translocations, rearing in captivity).