Numerous native European freshwater crayfish populations are in decline due to the lethal disease crayfish plague caused by the pathogen Aphanomyces astaci (Oomycetes). Presence of this pathogen has already been recorded in the Plitvice Lakes National Park (NP), Croatia, where two protected native crayfish species, the noble crayfish Astacus astacus and the stone crayfish Austropotamobius torrentium occur. Data presented in this manuscript are part of a two-year monitoring project of the pathogen in the NP. Previously, we have reported the overall prevalence of A. astaci positive individuals in A. astacus and A. torrentium populations (14% and 2% of tested crayfish, respectively) within the NP. Here, we report the detailed distribution of the pathogen within the NP and differences in its prevalence in populations of both crayfish species collected at different locations within the NP. Moreover, we have identified the A. astaci genotype present within the NP and discuss our findings in the context of crayfish plague related management activities in the NP. The majority of pathogen records were from the A. astacus populations which were all in close proximity, and this presumably facilitated the pathogen spread among them. Prevalence of A. astaci positive A. astacus varied in different populations from 10% to 18%. In comparison, only one out of three tested A. torrentium populations, in the proximity of the A. astacus populations, was A. astaci positive (prevalence 17%), while in the other two geographically distant populations pathogen was not recorded. The microsatellite genotyping identified the presence of A. astaci haplogroup A (As genotype). Although known for its low virulence, A. astaci of haplogroup A could still cause mass mortalities, especially if combined with other stressors that can impair crayfish health. Obtained results were used as a baseline for the development of monitoring protocol for A. astaci and were incorporated in the management plan for protection of vulnerable native species in the NP. We present the proposed management activities for prevention of unintentional spread of the crayfish plague pathogen to adjacent streams that are inhabited by pathogen free native crayfish populations