The purpose of the present study was to investigate the prevalence and molecular characterization of Giardia duodenalis among dogs in Aydin, Turkey. A total of 473 faecal samples from dogs were collected. The overall prevalence of G. duodenalis was 18.8%. Higher infection rates were observed in dogs younger than three months old, from shelters, and with diarrhoea. Faecal samples of 89 dogs, diagnosed Giardia-positive by microscopy, were found positive by nested PCR. The β-giardin nested PCR assay revealed assemblage B in all samples (100%), whereas 38 of the samples were mixed with assemblage A (42%). Sequence analysis of isolates indicated sub-genotypes A3 and B4 which have been previously detected in human isolates from Turkey. The results of the present study indicated the relatively high prevalence of giardiasis and the presence of the zoonotic sub-genotypes suggesting the important role of dogs as potential reservoirs of human infections.