Giardia duodenalisis a common enteric parasite in humans and animals. To examine the occurrence and genetic characteristics of Giardiain donkeys in Xinjiang, China, 758 fecal samples from donkeys were collected, and Giardiawas screened via PCR at the SSUrRNA gene. A total of 17.0% (129/758) of samples tested positive for Giardia, with the infection rate in large-scale farm and domestic donkeys being 21.4% (124/580) and 2.8% (5/178), respectively; the infection rates in <1-year-old and ≥1-year-old donkeys were 19.3% (72/374) and 12.7% (41/323), respectively. Three Giardiaassemblages were identified, with assemblage B (n= 102) as the prevalent assemblage, followed by assemblage A (n= 23) and assemblage E (n= 4). Of the 129 Giardia-positive isolates, 40, 34 and 59 sequences were obtained at the bg, gdhand tpigenes, respectively. Twenty-one isolates successfully allowed multilocus genotyping (MLG), with four novel assemblage A MLGs, named MLG-AI-1 (n= 1), MLG-AI-2 (n= 1), MLG-AI-3 (n= 1), and MLG-AI-4 (n= 1) and three novel assemblage B MLGs, named MLG-B1 (n= 1), MLG-B2 (n= 14), and MLG-B3 (n= 1). Moreover, two isolates formed two MLG-mixed sequences. The results suggest that donkeys are commonly infected with Giardiain Xinjiang, and there is genetic diversity and host adaptability among the isolates.