Technical Abstract: The merozoite surface antigen-2 (msa-2) family of Babesia bovis is a group of variable genes that share conserved 5' and 3' ends and encode for membrane-anchored glycoproteins that have been postulated as vaccine candidates. In this work, we analyzed the sequences of three of these genes (msa-2a1, a2, and 2b) from two geographically distant strains and detected a certain degree of genotypic diversity that could be exploited to work out new molecular tools for the discrimination of B. bovis field samples. Here we describe a PCR restriction assay that was developed based on this observation and tested on several B. bovis strains and isolates. The results show a strain-specific band pattern in geographically distant isolates, indicating the presence of differentially located BspMI restriction sites. This approach provides a simple method for the differentiation of American B. bovis strains.