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<i>Blastocystis</i> spp. and <i>Giardia duodenalis</i> are two prevalent zoonotic intestinal parasites that can cause severe diarrhea and intestinal diseases in humans and many animals. Black goat (<i>Capra hircus</i>) farming is increasingly important in China due to the remarkable adaptability, high reproductive performance, rapid growth rate, and significant economic value of black goats. A number of studies have indicated that black goats are the potential reservoir of multiple zoonotic protozoans in China; however, the prevalence and zoonotic status of <i>G. duodenalis</i> and <i>Blastocystis</i> spp. in black goats in Shanxi Province is still unknown. Thus, a total of 1200 fecal samples of black goats were collected from several representative regions at different altitudes in Shanxi Province and were examined for the presence and genotypes of <i>G. duodenallis</i> and <i>Blastocystis</i> spp. by amplifying the beta-giardin (<i>bg</i>), glutamate dehydrogenase (<i>gdh</i>), and triosephosphate isomerase (<i>tpi</i>) loci of <i>G. duodenalis</i> and SSU rRNA of <i>Blastocystis</i> spp. using PCR and sequence analysis methods, respectively. The overall prevalence of <i>G. duodenalis</i> and <i>Blastocystis</i> spp. in black goats in Shanxi Province were 7.5% and 3.5%, respectively. Two assemblages (B and E) of <i>G. duodenalis</i> and four subtypes (ST5, ST10, ST14, and ST30) of <i>Blastocystis</i> spp. were identified, with assemblage E and ST10 as the prevalent genotype and subtype in black goats, respectively. One novel multilocus genotype (MLG) was identified in MLG-E and was designated as MLG-E12. For both <i>G. duodenalis</i> and <i>Blastocystis</i> spp., the prevalence was significantly related to the region and age groups (<i>p</i> < 0.05). This is the first report on the prevalence of <i>G. duodenalis</i> and <i>Blastocystis</i> spp. in black goats in Shanxi Province. These results not only provide baseline data for the prevention and control of both parasites in black goats in Shanxi Province, but also enhance our understanding of the genetic composition and zoonotic potential of these two parasites.