Austropotamobius pallipes complex is an endangered freshwater crayfish species in Europe and the assessment of the health status of its wild populations is essential for conservation purposes. The two microsporidia Astathelohania contejeani and Nosema austropotamobii have been reported to cause in A. pallipes complex a chronic parasitic infection, known as ‘porcelain disease’, which reduces population fitness and leads the host to death. Due to the similar macroscopic signs produced, molecular biology analyses are required to unambiguously distinguish between these microsporidia. Focusing on A. pallipes complex populations located in Northern and Central Italy, the present study provides an evaluation of prevalence and distribution of A. contejeani and N. austropotamobii, and investigates the variables affecting the probability of detecting infected specimens during a survey (e.g. sex, crayfish density, longitude). Microsporidia were identified in 12 populations among the 42 monitored from 2011 to 2017, with an average prevalence of 3.12% for A. contejeani and 3.60% for N. austropotamobii, the latter being reported in a wider area than previously documented (from Lombardy to Liguria Regions). Notably, crayfish co-infected by both microsporidia were also detected in 4 populations. Moreover, it was observed that the probability of detecting a crayfish with a microsporidian infection significantly increased eastwards in the studied area, especially for N. austropotamobii. Our distribution map for microsporidiosis, combined with molecular screening, will be useful for planning breeding and translocation efforts for A. pallipes complex populations.