Giardia duodenalis is an intestinal pathogen that is found globally. Children are more susceptible and often suffer severe consequences after infection. Despite this, the health effects of this pathogen continue to be poorly understood and neglected. In Wenzhou, Zhejiang province, China, stool samples were obtained from 1032 children who were admitted to Yuying Children's Hospital. Out of these, 684 presented with diarrhea, while 348 were asymptomatic. The stool samples were screened for G. duodenali by targeting the small subunit of the ribosomal RNA (SSU rRNA) gene. Subtypes of G. duodenalis were identified via amplification of the glutamate dehydrogenase (gdh), beta-giardin (bg), and triosephosphate isomerase (tpi) genes in samples positive for the G. duodenalis. The findings indicated the presence of G. duodenalis in 0.9 % (9/1032) of the samples, with 9/684 (1.3 %) of the samples originating from children with diarrhea and none from the asymptomatic samples. All 9 samples that tested positive for G. duodenalis were determined to be of assemblage A. Of these, 6 samples were effectively genotyped at all 3 loci, resulting in the identification of 3 distinct MLGs: MLG-AII1 (n = 1), MLG-AII2 (n = 4), and MLG-AII2 (n = 1), all belonging to G. duodenalis assemblage AII. This was the first study that confirmed G. duodenalis infections in children residing in southern Zhejiang, China, with comparatively low rates of infection. The detection of G. duodenalis assemblage AII indicates a possibility of transfer from one human to another. The parasite's effect on the health of young children requires special attention and consideration.