Abstract Shigella sonnei is an emergent cause of diarrheal disease in middle-income countries. The organism causes endemic disease and is also associated with sporadic outbreaks in susceptible populations. In 2010 and 2011 there were two suspected outbreaks of diarrheal disease caused by S. sonnei in La Pampa province in central Argentina. Aiming to confirm these as outbreaks and provide insight into the relationship of the strains causing these infections we combined antimicrobial susceptibility testing and pulsed field gel electrophoresis (PFGE) with whole genome sequencing (WGS). Antimicrobial susceptibility testing suggested the two events were unrelated; organisms isolated in 2010 exhibited resistance to trimethoprim sulphate whereas the 2011 S. sonnei were non-susceptible against ampicillin, trimethoprim sulphate and cefpodoxime. PFGE profiling confirmed the likelihood of two independent outbreaks, separating the isolates into two main XbaI restriction profiles. We additionally performed WGS on 17 isolates associated with these outbreaks. The resulting phylogeny confirmed the PFGE structure and separated the organisms into two comparatively distantly related clones. Antimicrobial resistant genes were common, and the presence of an OXA-1 was likely associated with resistance to cefpodoxime in the second outbreak. We additionally identified novel horizontally transferred genetic material that may impinge on the pathogenic phenotype of the infecting strains. Our study shows that even with a lack of supporting routine data WGS is an indispensible method for the tracking and surveillance of bacterial pathogens during outbreaks and is becoming a vital tool for the monitoring of antimicrobial resistant strains of S. sonnei.