BACKGROUND: Cryptosporidium spp., Enterocytozoon bieneusi, and Blastocystis sp. are common enteric parasites in humans and pigs. Ascertaining whether non-biting flies (NBFs) serve as potential vectors of these parasites on pig farms is a crucial aspect of disease control. METHODS: Non-biting flies were collected and identified by morphology analysis together with sequence analysis of the mitochondrial cytochrome c oxidase I (CO1) gene as confirmation. In a cross-sectional study, the small-subunit ribosomal RNA (SSU rRNA) gene of Cryptosporidium spp., the internal transcribed spacer region (ITS) region of E. bieneusi and the SSU rRNA gene of Blastocystis sp. were investigated in fresh pig fecal samples and sympatric NBFs. RESULTS: The results revealed the occurrence of five species of NBFs (Musca domestica, 91.2%; Lucilia sericata, 5.8%; Chrysomya megacephala, 1.7%; Aldrichina grahami, 0.6%; Helicophagella melanura, 0.6%) in the collected pig fecal samples. The prevalence of Cryptosporidium spp., E. bieneusi and Blastocystis sp. on the body surface of NBFs was 0.6% (2/342), 4.4% (15/342) and 20.8% (71/342), respectively. Similarly, the prevalence of these parasites in the lysates of NBFs (= in vivo carriage) was 0% (0/342), 2.7% (9/342) and 10.5% (36/342), respectively. The prevalence of Cryptosporidium spp., E. bieneusi and Blastocystis sp. in pigs from which fly samples were collected was 2.3% (41/1794), 12.6% (226/1794) and 30.8% (553/1794), respectively. The zoonotic Cryposporidium suis/C. scrofarum, E. bieneusi ITS genotypes EbpA/EbpC and Blastocystis sp. subtypes ST1/ST3/ST5 were identified in both NBFs and pig feces. NBFs were found to carry E. bieneusi and Blastocystis sp. on their body surface as well as in the lysates. CONCLUSIONS: These findings demonstrate the role of NBFs as potential vectors in the dissemination of these zoonotic parasites in pig farms, and also highlight the possibility of their transmission to humans.