Piroplasmosis was first described in raccoons (Procyon lotor) in 1926, and the official description of a small piroplasm as Babesia lotori was done in 1981. Babesia microti-like gene sequences have been characterized in raccoons in both North American and Japan. It is well documented that the microscopic appearance of piroplasms does not always accurately predict the genotype and phylogenetic classification. Discrepancies using phenotype to predict genotype have been reported most frequently when evaluating small piroplasms. We amplified and sequenced the full-length 18S rRNA gene from a small piroplasm identified in a raccoon and used this sequence for phylogenetic analyses. Based on these analyses, the organism was placed in the Babesia sensu stricto clade, confirming that it is a true Babesia sp. This documents that at least two Babesia spp. can infect raccoons. The data generated in this study can be used to design molecular diagnostic tests for detection of this Babesia sp., which will be useful for epidemiologic and comparative phylogenetic studies. As piroplasmosis has been documented with increased frequency in humans in recent years, the results of this study will aid in the recognition of zoonotic babesiosis.