Tissue cysts of Besnoitia sp. were found in muscles and several organs from a naturally infected Akodon montensis captured in the rural area of the municipality of Timbó, Santa Catarina State, in southern Brazil. Indirect fluorescence and enzyme-linked immunosorbent assays carried out with sera from mice chronically infected with Toxoplasma gondii and Besnoitia sp. showed, as expected, a stronger reaction against homologous than heterologous antigens. No cross-protection was observed in mice immunized with T. gondii when challenged with Besnoitia sp. This is the first description of a natural infection of A. montensis by parasites of the genus Besnoitia sp. in Brazil.