Toxoplasma gondii and Neospora caninum are closely related coccidian parasites infecting a wide range of wild and domestic animals as intermediate hosts, and rodents serve as important reservoir hosts during the life cycles of these parasites. The present study is aimed at identifying T. gondii and N. caninum infection in 360 wild house mice (Mus musculus) collected across the Czech-German border, where 2 genetically distinct mouse subspecies meet and hybridize. Toxoplasma gondii or N. caninum DNA was detected in the brains of individual mice by PCR, but mixed infections were never observed. No significant differences in gender or trapping localities were found in the positive mice. The survey reveals a low frequency of T. gondii (0.6%) and N. caninum (3.6%) occurrence in the house mice population of the monitored part of the hybrid zone.