Enterocytozoon bieneusi is an opportunistic microsporidian parasite with zoonotic potential that causes gastrointestinal illness in humans and animals. This study aimed to investigate the presence and genetic diversity of E. bieneusi from cats in Korea and to assess the potential public health risks associated with zoonotic genotypes. Among the 137 feline fecal samples, 4 (2.9%) were PCR-positive for E. bieneusi. In addition, 2 E. bieneusi genotypes were identified: Type IV, a known zoonotic genotype belonging to Group 1, and KCAT1, a novel genotype with zoonotic potential belonging to Group 1. This study is the first to report on these genotypes from cats in Korea, most of which were companion cats visiting veterinary clinics. Despite the low detection rate, the presence of zoonotic genotypes in companion cats is a potential public health concern because of the close physical interaction between cats and their human caregivers. These findings indicate the importance of routine monitoring and the molecular characterization of E. bieneusi in companion animals to comprehensively understand their zoonotic transmission patterns and to guide future risk assessments and preventive strategies.