Multi-locus typing scheme for Babesia bovis and Babesia bigemina reveals high levels of genetic variability in strains from Northern Argentina

► We developed two multi locus typing schemes for Babesia bovis and B. bigemina. ► Both schemes showed excellent discrimination power. ► High levels of genetic diversity and infections with multiple genotypes were found. ► Linkage disequilibrium analysis and lack of congruence in phylogenetic trees suggest recombination events.