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<i>Streptococcus zooepidemicus</i> is an emerging zoonotic pathogen involved in septicemic infections in humans and livestock. Raising guinea pigs in South America is an important economic activity compared to raising them as pets in other countries. An outbreak of severe lymphadenitis was reported in guinea pigs from farms in the Andean region. <i>S. zooepidemicus</i> was isolated from multiple cervical and mandibular abscesses. Isolate was characterized by multilocus sequence typing and phylogenetic analysis. This is the first molecular characterization of a highly pathogenic strain, showing major important virulence factors such as the M-like protein genes <i>szP</i> and <i>mlpZ</i>, the fimbrial subunit protein gene <i>fszF</i>, and the protective antigen-like protein gene <i>spaZ.</i> Additionally, this guinea pig strain was phylogenetically related to equines but distant from zoonotic and pig isolates reported in other countries.