Rodents (Mammalia: Rodentia) are among the ubiquitous hosts of Giardia duodenalis, as they can harbour at least six assemblages of this species, including the zoonotic assemblages A and B. However, studies targeting a broad spectrum of rodents and rabbits sampled in the same region are scarce, even in Europe. During this study, 164 samples were collected from five rodent species and rabbits in five locations in Hungary, to examine the presence of G. duodenalis with traditional parasitological and molecular methods. Parasitological analysis revealed the presence of cysts in 58.3% of asymptomatic Norway rats and 27.6% of chinchillas. Three degus were also found Giardia-infected (prevalence: 16.7%) using flotation technique. With PCR targeting three genetic markers, 3.2% of the samples showed positivity, whereas a rate of 21.9% prevalence was detected with flotation. The PCR products of five samples could be DNA sequenced. Phylogenetic analysis based on the partial sequences of the beta-giardin gene revealed the presence of assemblages B and G in rats. In addition, assemblage E was detected in a beaver, while assemblage B was present in a chinchilla. The results show that synanthropic rodent species have different epidemiological roles in the study region, depending on the prevalence of shedding Giardia cysts or harbouring zoonotic variants of G. duodenalis. Moreover, our findings confirm that pet rodents may pose a risk for zoonotic Giardia-transmission.