Cryptosporidium species and microsporidia, which can cause zoonotic intestinal infections in humans, have become an emerging public health concern. It seems that the identification and genotyping of these parasites are necessary for the prevention, control, and establishment of appropriate treatment. This study aimed to evaluate the distribution and zoonotic transmission routes of Cryptosporidium species and microsporidia to humans referred to medical laboratories of Kurdistan Province, Iran. A total of 1,383 stool samples were collected and investigated. Cryptosporidium spp. and microsporidia were detected using microscopic methods (i.e., formol-ether concentration, Ziehl-Neelsen staining, and modified trichrome staining methods). DNA was extracted from positive samples, and specific fragments of the Cryptosporidium GP60 gene and microsporidia SSU rRNA gene were amplified. Furthermore, positive samples were sequenced for genotype identification and bioinformatics analysis. Based on the microscopic analysis of 1,383 stool samples, 5 (0.36%) and 6 (0.43%) samples were considered positive for Cryptosporidium oocysts and microsporidia spores, respectively. Molecular analysis of positive samples identified the isolates as Cryptosporidium parvum and Enterocytozoon bieneusi. According to comparative phylogenetics, cryptosporidiosis and microsporidiosis may occur via zoonotic transmission in this region. Therefore, proper control and health education are strongly recommended to prevent zoonotic diseases.

隐孢子虫种和微孢子虫可引起人类的人畜共患肠道感染，已成为新出现的公共卫生问题。这些寄生虫的鉴定和基因分型似乎对于预防，控制和建立适当的治疗是必要的。这项研究旨在评估伊朗库尔德斯坦省医学实验室隐孢子虫和微孢子虫对人的分布和人畜共患的传播途径。总共收集和调查了1,383份粪便样品。隐孢子虫spp。使用显微镜方法（即，甲醚浓度，Ziehl-Neelsen染色和改良的三色染色方法）检测孢子虫和小孢子虫。从阳性样品中提取DNA，并扩增隐孢子虫GP60基因和微孢子虫SSU rRNA基因的特定片段。此外，对阳性样品进行测序以进行基因型鉴定和生物信息学分析。根据对1,383份粪便样品的显微镜分析，分别认为隐孢子虫卵囊和微孢子虫孢子呈阳性的分别为5（0.36％）和6（0.43％）。阳性样品的分子分析鉴定为小隐隐孢子虫和比氏肠杆菌。根据比较的系统发育学，隐孢子虫病和微孢子虫病可通过人畜共患病传播在该区域发生。因此，强烈建议进行适当的控制和健康教育，以预防人畜共患疾病。