Background and Aim: In Indonesia, Madura cattle are native breeds that are expected to contribute to the improvement of regional meat self-sufficiency. Eimeria spp. are protozoans that are commonly found in ruminants. This study aimed to identify the occurrence and diversity of Eimeria spp. in Madura cattle.

Materials and Methods: In this study, fresh fecal samples were collected from 100 cattle in Kamal Subdistrict, Bangkalan District, Madura Island, Indonesia. Morphological detection was performed using a light microscope, and molecular identification was performed using a polymerase chain reaction. DNA amplification was conducted using various species-specific primers for Eimeria bovis, Eimeria zuernii, Eimeria auburnensis, Eimeria alabamensis, Eimeria ellipsoidalis, and Eimeria cylindrica.

Results: The results obtained 21% (21/100) of Eimeria spp. based on morphological detection. A total of 15 positive samples with 500–25,000/mL oocysts were selected for DNA extraction and amplification, resulting in 12 positive samples. Four Eimeria spp. were obtained based on molecular identification: E. bovis, E. zuernii, E. auburnensis, and E. cylindrica.

Conclusion: Four species of Eimeria namely E. bovis, E. zuernii, E. auburnensis, and E. cylindrica were identified from fecal sample of Madura cattle using PCR method in this study. Further comprehensive studies are required to investigate the pathogenicity of Eimeria spp. in Madura cattle. Therefore, improved and integrated management practices should be strengthened by local governments to prevent pathogenic diseases and increase national livestock productivity in Indonesia.

Keywords: biodiversity, Eimeria species, infectious disease, Madura cattle, Madura Island.