Besnoitia besnoiti tissue cysts from a recent outbreak in cattle in Germany were characterized with respect to their internal transcribed spacer regions 1, 2, and 18S rDNA gene sequences. These results were compared with own sequences of an Israelian isolate of B. besnoiti and of Besnoitia jellisoni cystozoites stored for years in liquid nitrogen. Furthermore, material was studied that was obtained from white mice (Balb/C) that had been successfully infected by intraperitoneal infection of fresh cystozoites from the German outbreak. All results were then compared and discussed with respect to databank sequences of other Besnoitia species. Comprehensive phylogenetic studies of B. besnoiti isolates from Germany revealed almost identical sequence alignments when compared to previously sequenced B. besnoiti isolates from Israel and Spain. More importantly, phylogenetic analysis revealed two distant clusters of Besnoitia species: the first one includes Besnoitia akodoni, Besnoitia darlingi, and Besnoitia oryctofelisi, while the second cluster includes B. besnoiti, Besnoitia bennetti, Besnoitia tarandi, and the Besnoitia species of rodents (B. jellisoni). The also B. jellisoni named species of the GenBank (AF 076860) must be another one, since our strain derives directly from Frenkel. These findings give strong hints that B. besnoiti has a cycle between rodents and a predator and that cattle and other are only accidental hosts.