Technical Abstract: The epidemiology of Eimeria species in poultry flocks is important to increase the effectiveness of vaccinations and prophylactic strategies on chicken farms. In this study, fecal samples from 356 chicken farms were collected randomly and examined for the prevalence of Eimeria species. Through microscopic examination, it was determined that 78.7% of the tested farms contained Eimeria-infected animals. All seven Eimeria species were detected by PCR amplification of the internal transcribed spacer 1 (ITS-1) region with species-specific primers. E. acervulina and E. tenella were the most prevalent, followed by E. brunetti and E. praecox (87.5%, 62.5%, 59.3%, and 37.5% of farms, respectively). Each of E. maxima, E. mitis, and E. necatrix was identified in 31.3% of farms. Multiple Eimeria species (mean = 3.4) were observed in individual positive fecal samples. Since E. maxima generates antigenic variants, cross-immunity was investigated for four isolates of E. maxima from poultry farms in different regions of Korea. The extent of cross-protection varied from 54.3% to 100% against the heterologous isolates. The results obtained from this large-scale survey will be a useful reference for controlling coccidiosis within the poultry industry.