This case report describes a patient with two simultaneous liver abscesses caused by two different strains of Entamoeba histolytica, as identified by polymorphisms in the chitinase gene. The patient presented with abdominal pain and fever and imaging showed large abscesses in the left and right liver lobes. Samples from draining each abscess revealed different chitinase genotypes, suggesting infection by two genetic variants of E. histolytica. This is one of the first reports of the co-existence of multiple strains of E. histolytica in the same patient.