European pond turtle, Emys orbicularis are an essential component of freshwaters and marshes cenoses and evaluation of parasites in their populations is essential for the management of conservation processes. Coccidiosis is the most common intestinal infection in free-living and captive reptiles. The aim of this study was to characterize the presence of Eimeria sp. in European pond turtle. Faecal samples were examined for the presence of coccidian oocysts by the standard flotation technique with saturated sodium chloride (NaCl; sp.gr. 1.18). A Leica DM1000 microscope equipped with the Leica DFC425 camera and ImageScopeTM Image Analysis Software was used for identification of found coccidia. Coproparasite examinations revealed the presence of two types oocysts of Eimeria in one of six fecal samples (16.6%) analyzed by flotation technique: E. gallaeciaensis and E. emydis. In addition, this is the first report of Eimeria in E.orbicularis in Azerbaijan. The morphological and statistical parameters of both species were determined and a comparative analysis was carried out with data from other authors. The presence of Coccidian can be the cause of enteritis and death in young tortoises. The source of coccidiosis infection in European pond turtle could be attributed to contamination of food and water.