Recently, two strains of a novel enterohepatic Helicobacter species, H. equorum, were isolated from fecal samples of two clinically healthy horses in Belgium. The purpose of the present study was to detect the presence of H. equorum infection in fecal samples of adult horses from Jeju Island using polymerase chain reaction (PCR). A total of 86 fecal samples from 31 clinically healthy Thoroughbred horses and 55 horses native to the Jeju Island were evaluated. H. equorum DNA was detected in 10.9% (6/55) of the native-horses, while all the Thoroughbred horses showed negative PCR results. Ages of the H. equorum DNA-positive horses ranged from 2 to 4 years old. To the best of our knowledge, this is the first study of H. equorum detection in fecal samples from horses in Korea.