Giardiasis is a notifiable disease of high prevalence in New Zealand, but there is limited knowledge about the sources of Giardia duodenalis genotypes that can potentially cause human infections. Dairy calves are one environmental source of Giardia isolates, but it is unknown whether they harbor genotypes that are potentially capable of causing infections in humans. To address these questions, 40 Giardia isolates from calves and 30 from humans, living in the same region and collected over a similar period, were genotyped using the β-giardin gene. The G. duodenalis genetic assemblages A and B were identified from both calves and humans, and genotype comparisons revealed a substantial overlap of identical genotypes from the two hosts for both assemblages. Significantly, no assemblage E (the genotype commonly found in cattle elsewhere in the world) has been detected in New Zealand livestock to date. Given recent and rapid land use conversions to dairy farming in many South Island regions of New Zealand, an increasingly large concentration of domestic cattle harboring genotypes potentially capable of causing infections in humans is particularly concerning.