Giardia duodenalis is a zoonotic parasite that causes gastrointestinal diseases in both humans and animals. To evaluate the prevalence and genetic diversity of G. duodenalis in black goats, we collected 539 fecal samples from nine districts in Fujian Province, China. The presence of G. duodenalis was confirmed through nested PCR targeting the SSU rRNA gene, and genotyping was performed at the beta-giardin, glutamate dehydrogenase, and triosephosphate isomerase loci. Among the samples, 115 tested positive, yielding an overall infection rate of 21.34%. Assemblages A and E were identified, with assemblage E being predominant. Statistical analysis revealed significant regional differences in infection rates (p G. duodenalis in black goats and provides critical data for the development of targeted control strategies in Fujian Province.