Giardia duodenalis is one of the major diarrhea agents in human and animals distributed worldwide, and present high levels of genetic diversity, showing seven genotypes: A, B, C, D, E, F, and G. Only Assemblages A and B have been detected in humans and in a wide range of other mammalians hosts, whereas the remaining Assemblages (C–G) are host-specific. Molecular characterization of cysts of human and animal origin are useful to address the co-circulate isolates between these host, and represents an objective means to evaluate zoonotic infection hypothesis. In the present work the G. duodenalis genotypes were characterized by restriction fragment length polymorphisms and DNA sequencing analysis of PCR products of the β-giardin gene. The cysts were collected in the city of Rio de Janeiro, in Brazil, from a population composed by humans ( n = 366, 310 children and 56 adults), domestic animals ( n = 11) from a municipal daycare center in the surroundings of a slum and neighborhood medium–high class domestic animals ( n = 18). Parasitological exams were developed in human fecal samples. Parasites were found in 60% (186/310) and 66% (37/56) of the samples from children and adults, respectively. Among children's samples, 27.7% (86/310) were positive for G. duodenalis. Only 1.7% (1/56) of the adults was positive for this parasite. In general a total of 87 fecal samples (86 from children and 1 from adult) from all population studied were positive for G. duodenalis, and 62 of these were subjected to molecular analysis using a PCR that amplified a fragment of the β-giardin gene. Sixty samples were typed as genotype A1, two as genotype A2 and genotype B was not encountered. Among domestic animals samples ( n = 29), eight (seven dogs and one cat) from the slum community were identified as genotype A1, and all control samples ( n = 18) were negative in the molecular assay. The host-specific genotypes C, D and, F were not found. In this study we described single case of G. duodenalis infection associated with a child and her dog and both isolates characterized as genotype A1. Despite the low incidence, this data suggest the putative existence of a zoonotic cycle of G. duodenalis in the studied population.