Caprine coccidiosis is an economic disease in goat husbandry. The study aimed to investigate the prevalence of caprine coccidiosis in the Mekong Delta, Vietnam, and characterization E. arloingi that is one of the most pathogenic and mobile among caprine Eimeria species. Our findings showed that 218 tested samples out of 251 had the presence of Eimeria species, accounting for 86.85 %. The highest infection rate of coccidiosis was recorded in goat kids (< 4-month- old goats) with 96.25%, followed by 88.61% in 4-12 month-old goats and 77.17% in > 12- month-old goats. Four various Eimeria species were morphologically identified, including E. arloingi (43.42%), E. ninakohlyakimovae (39.84%), E. christenseni (33.86%), E. alijevi (12.75%). Molecular characterization of E. arloingi was performed based on two different genes, namely internal transcribed spacer-1 (ITS-1) and 18S rDNA. The phylogenetic trees revealed that E. arloingi had a close relationship to other Eimeria species from goat and sheep. This study confirmed that ITS-1 and 18S rDNA are appropriate genetic markers in the identification and differentiation of Eimeria species in small ruminants.