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<i>Blastocystis</i> spp., <i>Enterocytozoon bieneusi</i>, and <i>Giardia duodenalis</i> are three common zoonotic intestinal parasites that cause severe diarrhea and enteric diseases. Leizhou black goats are characterized by a high reproductive rate, fast growth, and good meat quality, making them one of the pre-eminent goat breeds in China. Goats are reportedly common reservoirs of these three intestinal pathogens, but no information on their prevalence or genotypic distributions in black goats in Guangdong Province, China, is available. A total of 226 fecal samples were collected from goats in Zhanjiang city and genomic DNA was extracted from them. The presence of the three pathogens was detected using nested PCR targeting the sequences encoding SSU rRNA (<i>Blastocystis</i> spp.), the internal transcribed spacer of rRNA (ITS; <i>E. bieneusi</i>), as well as beta-giardin, glutamate dehydrogenase, and triosephosphate isomerase (<i>G. duodenalis</i>). All PCR products were sequenced to determine the species and genotypes of the organisms. The total prevalence rates of <i>Blastocystis</i> spp., <i>E. bieneusi</i>, and <i>G. duodenalis</i> were 33.63% (76/226), 17.70% (40/226), and 24.78% (56/226), respectively. Four subtypes of <i>Blastocystis</i> spp. were detected: ST5 (<i>n</i> = 6), ST10 (<i>n</i> = 50), ST14 (<i>n</i> = 14), and ST21 (<i>n</i> = 6). Among them, ST10 was the dominant genotype, accounting for 65.79% of strains, followed by the genotypes ST14 (18.42%), zoonotic ST5 (7.89%), and ST21 (7.89%). Four genotypes of <i>E. bieneusi</i> were detected: CHG3 (<i>n</i> = 32), CM21 (<i>n</i> = 4), CHG1 (<i>n</i> = 2), and ET-L2 (<i>n</i> = 2). Among these, CHG3 was the dominant genotype. Assemblage E (<i>n</i> = 54) and concurrent assemblages A and E (<i>n</i> = 2) were identified in the <i>G. duodenalis</i>-positive goats using multilocus genotyping. <i>Blastocystis</i> spp., <i>E. bieneusi</i>, and <i>G. duodenalis</i> infections were common in Leizhou black goats, all of which have zoonotic genotypes, indicating the potential risk of zoonotic transmission. Our results provide basic data for the prevention and control of these three intestinal pathogens. Further studies are required to better understand their genetic characteristics and zoonotic potential in Guangdong Province.