Abstract
Background:
Coccidiosis caused by Eimeria species (spp.) is a significant global health concern in goats leading to gastrointestinal illness. This condition causes clinical manifestations, including weight loss and diarrhea, resulting in worldwide economic losses. Subclinical symptoms can manifest during Eimeria infection. Neglecting this disease can lead to severe morbidity and mortality. Therefore, addressing caprine coccidiosis is imperative.

Aim:
This study aimed to determine the prevalence and molecular identification related to the natural infection of Eimeria spp. in domestic goats originating from Java Island, Indonesia.

Methods:
In total, fecal samples from 289 domestic goats were obtained across five provinces on Java Island, Indonesia: East Java, Central Java, D. I. Yogyakarta, West Java, and Banten. Morphological examinations were performed using the modified Whitlock method and saturated sugar flotation. Molecular assays targeting the 18S ribosomal ribonucleic acid have been employed for spp.-specific confirmation. Statistical analysis was performed using the Wilson binomial proportion and chi-square methods implemented in the online software.

Results:
A total of 92.7% (268/289) of fecal samples tested positive for Eimeria spp. Phylogenetic tree analysis demonstrated that Eimeria christenseni and E. arloingi closely resembled the reference sequences from China, Australia, and other countries.

Conclusion:
This study identified Eimeria christenseni and Eimeria arloingi as the goat-infecting spp. of Eimeria present on Java Island. The specific and accurate molecular identification conducted in this study will contribute to improved coccidiosis control and the development of effectiveness.

Key words: Eimera, Goat, Indonesia, Molecular identification, 18S rRNA