The use of mass antimicrobial treatment has been linked to the emergence of antimicrobial resistance in human and animal pathogens. Using whole genome (SMRT) sequencing, we characterized genomic variability of multidrug-resistant R. equi isolated from soil samples from 100 farms endemic for R. equi infections in Kentucky. We discovered the novel erm(51) encoding resistance to MLSB in R. equi isolates from soil of horse-breeding farms. erm(51) is inserted in a transposon (TnErm51), that is associated either with a putative conjugative plasmid (pRErm51), a mobilizable plasmid (pMobErm51), or both enabling horizontal gene transfer to susceptible organisms and conferring high levels of resistance against MLSB in vitro. This new resistant genotype also carries 2 previously unidentified rpoB mutations conferring resistance to rifampicin. Isolates carrying both vapA and erm(51) were rarely found, indicating either a recent acquisition of erm(51) and/or impaired survival when isolates carry both genes. Isolates carrying erm(51) are closely related genetically and were likely selected by antimicrobial exposure in the environment. This article is protected by copyright. All rights reserved.