In a recent study of intestinal parasites in dogs and cats in Australia, Giardia was found to be the most prevalent parasite in dogs. The aim of the current study through the use of molecular tools was to determine the zoonotic significance of the Giardia and Cryptosporidium isolates recovered from dogs and cats during the Australian study. Of the isolates successfully amplified all but one of the Giardia from dogs was either Assemblage C and/or D, with one Assemblage A. Of the cat samples amplified all but one were Assemblage F, with one Assemblage D. We hypothesize that the lack of zoonotic Giardia Assemblages recovered is a result of their being a low prevalence of Giardia in the human population. The Cryptosporidium recovered from dogs and cats was determined to be C. canis and C. felis, respectively, a finding which supports growing evidence that Cryptosporidium in companion animals is of limited public health significance to healthy people.