Encephalitozoon cuniculi has a wide host range among mammals, but whether it represents a homogeneous species is a subject of controversy. We have isolated, cultivated (in human MRC-5 cells) and, for the first time, characterized by immunological and molecular biological methods four isolates of E. cuniculi from Norwegian blue foxes with a history of encephalitozoonosis. The isolates were compared with nine isolates from domestic rabbits from Switzerland. Two E. cuniculi subtypes were identified according to their host species. A 5'-GTTT-3' tetranucleotide repeat was present twice in the rDNA intergenic spacer in all isolates from foxes as opposed to three times in all isolates from rabbits. Furthermore, random amplified polymorphic DNA analysis showed one polymorphic band among the subtypes, and Western-blot analysis using serum from an infected fox discriminated between the two subtypes on the basis of their banding patterns in the ranges of 31-33 and 38-40 kDa. The 5'-GTTT-3' tetranucleotide repeat is a valuable genetic marker for these two subtypes of E. cuniculi and will be of use in continued studies on the molecular epidemiology of this parasite.