Branchiobdellid annelids are usually found as commensal symbionts associated with crayfish populations, but knowledge of their dispersion and ecology in Europe is generally scarce. We hypothesized that their geographic extension of species and populations may mirror the distribution history of their hosts. We analysed potential host specificities and the geographic distribution of species from the Italian and Austrian Tyrol and Carinthia by characterizing the morphological and genetic features. On the three indigenous crayfish species Astacus astacus, Austropotamobius pallipes and Austropotamobius torrentium, we identified four branchiobdellid species based on morphological characteristics: Branchiobdella hexodonta, Branchiobdella pentodonta, Branchiobdella balcanica and Branchiobdella parasita. In contrast to the morphological classification, phylogenetic analysis using mitochondrial cytochrome c oxidase I (CO-I) sequences identified five main lineages: B. balcanica, B. hexodonta, Branchiobdella italica, B. parasita and B. pentodonta. The arrangement of branchiobdellid species corresponded generally to the geographical distribution of their crayfish hosts' locations but also confirmed previous assumptions of crayfish translocations. Our study provides the first application of ideas on the association of freshwater crayfish and their ectosymbionts to be used for discussing the biogeography of crayfish populations. The phenotypical and genotypical analysis also demonstrated so far ignored effects of human activities at both macro-ecological and micro-ecological levels.