Echinostomes are common intestinal parasites causing zoonotic disease, which are endemic worldwide. Of the four species of medically important echinostomes reported in Thailand, two species, Echinostoma revolutum and Hypodereaum conoideum, have been detected in poultry. These two parasites are morphologically similar and are sometimes difficult to distinguish. In the present study, multilocus enzyme electrophoresis was used to differentiate E. revolutum from H. conoideum collected from domestic ducks in Thailand. The parasites were compared using 22 enzymes with 30 presumptive enzyme loci. The two species of echinostome could be distinguished at 17 of the 30 enzyme loci. Several loci were polymorphic within each species, suggesting that these can be used to examine their population genetics.