Babesia divergens and B. divergens-like organisms are the main causative agents of human babesiosis in Europe. Recently, the first case of human infection with Babesia microti was confirmed in Germany, implicating the presence of zoonotic isolates. To estimate the presence of zoonotic B. microti in Croatia we analyzed 120 small wild mammals that serve as its reservoir by polymerase chain reaction. Yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) were both found to be infected with prevalence of 16.2%. Sequence analysis of the portion of 18S rDNA gene demonstrated that six polymerase chain reaction-positive samples, detected in both rodent species, were identical to that of the human Jena/Germany strain (EF413181). The other two isolates were identical to the nonzoonotic Munich strain (AB071177). The results of this study indicate the presence of zoonotic B. microti in A. flavicollis and M. glareolus in Croatia and a potential risk for human health.