Erythrocyte-stage Babesia equi expresses a 34-kDa immunodominant antigen recognized by antibody from persistently infected horses worldwide. This erythrocyte-stage surface protein, equi merozoite antigen-1 (EMA-1) is encoded by a single copy gene, and was previously shown to share 33% amino acid identity with similar sized proteins of Theileria sergenti and T. buffeli. A mean homology of 31% amino acid identity extends to similar sized proteins of T. parva, T. annulata and T. mutans. Genomic and cDNA copies of a second B. equi gene, ema2 were cloned. The single copy ema2 gene encodes a 30-kDa protein (EMA-2) that shares 52% amino acid identity with EMA-1. EMA-2 also shares a mean amino acid identity of 31% with proteins of similar molecular mass from Theileria species. EMA-1 and EMA-2 each contain a glycosylphosphatidylinositol anchor. These unique erythrocyte-stage surface proteins of B. equi and Theileria species lack antigenic repeats, and excluding the signal peptide, contain one or no cysteines. Consistent with the hypothesis that this family of proteins interacts with the erythrocyte surface, the T. species proteins possess a basic isoelectric point. The B. equi proteins have acidic isoelectric points, but 24-mer peptides within them have strongly basic net charges.