| Summary: | Feral cats that are roaming outside can serve as reservoirs for zoonotic pathogens, negatively impacting public health. They may experience high levels of parasitic infection. Some gastrointestinal protozoa and microsporidia possessing zoonotic potential in cats include <i>Cryptosporidium</i> spp., <i>Giardia duodenalis</i>, <i>Blastocystis</i> sp., <i>Enterocytozoon bieneusi</i>, and <i>Toxoplasma gondii</i>. Here, we show the infection rates and risk factors of intestinal protozoa and microsporidia detected from shelter cats on Jeju Island in South Korea in 2020. Among 158 cats, we detected genes for five internal protozoa and microsporidia, namely, <i>Cryptosporidium felis</i> (0.6%), <i>G. duodenalis</i> (3.8%), <i>Blastocystis</i> sp. (0.6%), <i>E. bieneusi</i> (3.8%), and <i>T. gondii</i> (1.3%). Furthermore, 16 cats (10.1%) were PCR-positive for at least one protozoan or microsporidium. To our knowledge, this study is the first to describe the existence of <i>C. felis</i>, <i>G. duodenalis</i> assemblage F, <i>Blastocystis</i> sp. ST4 subtype, and <i>E. bieneusi</i> genotype Peru11 in cats in South Korea. Despite the small number of positive samples, this study expands our understanding of the incidence of zoonotic gastrointestinal protozoa and microsporidia in shelter cats and genetically characterizes the isolates found in the infected animals. Moreover, these findings emphasize the need for a better control strategy on protozoa and microsporidia in cats, tailored to their individual needs, to protect animal and public health.
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