Large piroplasms (>2.5microm) were detected by direct microscopical investigation in 34 out of 16,767 (0.20%) canine blood smears in the Southern region of Greater Buenos Aires. Genomic DNA was extracted from two parasitemic dogs and the hypervariable 18S RNA gene region of the pathogen was specifically amplified, sequenced, and aligned with corresponding gene sequences available in the GenBank. Phylogenetic trees were constructed and compared. 18S RNA gene sequences reliably segregated in three clearly distinguishable clades representing Babesia canis, Babesia vogeli and Babesia rossi isolates, respectively. The 18S RNA gene sequences of both Babesia isolates from Argentina affiliated to the B. vogeli branch. This finding represents the first molecular evidence of the existence of B. vogeli in Argentina.