Babesia merozoite polypeptides bear surface exposed and neutralization-sensitive B cell epitopes and have been shown to induce partial protection against experimental challenge. Variation in these epitopes has been examined in a limited number of strains. In this study, utilizing strains of Babesia bovis and Babesia begemina from Matto Grosso do Sul in Brazil, we examined the conservation of epitopes bound by monoclonal antibodies developed against Mexico strains of B. bovis and B. bigemina. Apical complex B-cell epitopes, previously shown to be species-specific but common among otherwise antigenically distinct strains, were also conserved between clones of the Mexico strains and the Matto Grosso do Sul strains of each Babesia species. Mexico strain polypeptides bearing these epitopes were recognized by sera from cattle infected with the Matto Grosso do Sul strains. Two distinct epitopes on the B. bovis neutralization-sensitive merozoite surface antigen-1 (MSA-1) were also conserved between the Mexico Mo7 clone and the Matto Grosso do Sul strain, in contrast to previous studies which demonstrated variability among strains. Sera from cattle with B. bovis infections naturally acquired in Matto Grosso do Sul bound Mexico Mo7 MSA-1, demonstrating that conserved MSA-1 epitopes were recognized by the bovine immune system. Similarly, merozoite surface epitopes on the B. bigemina 45 kDa and 55 kDa glycoproteins were conserved on the Matto Grosso do Sul strain of B. bigemina.