Background and aims Coccidian parasites, including Eimeria, present a significant challenge to wildlife due to their detrimental impacts. However, their precise identification remains complex, often leading to ambiguous 'Eimeria sp.' observations particularly within the context of the Alpine Marmot (Marmota marmota). This study aimed to elucidate the specific Eimeria species inhabiting Marmota marmota, and compare them with the species previously described within the Marmotini tribe. Methods We conducted fecal sample collection from Alpine Marmots in La Grande Sassière reserve, France, focusing specifically on samples containing Eimeria spp. oocysts. Using a sucrose flotation technique, these oocysts were isolated, allowed to sporulate, and then examined under a microscope. Guided by the principles set forth by Duszynski and Wilber, we undertook measurements and observations, supplementing these with morphometric studies for a thorough understanding of the coccidia. This approach facilitated the evaluation of polymorphism and the potential shape tendencies of the species. Results Through detailed analysis of observed oocysts, we distinguished two unique groups of coccidia, differentiated notably by oocyst and sporocyst size, as well as wall texture and color. These groups were labeled 'Large Eimeria' and 'Small Eimeria', with all marmots harboring Large Eimeria also evidencing the presence of Small Eimeria. Until now, these two species, the 'Large Eimeria' and 'Small Eimeria', had not been clearly described and named. By comparing these descriptions and photomicrographs with previously described species within the Marmotini tribe, we identified Eimeria lateralis and Eimeria monacis. Conclusions This study thus enabled us to provide a comprehensive and detailed description of the oocysts of these two species, complete with detailed diagrams and microphotographs. Additionally, we highlighted certain inconsistencies and confusions present within the literature describing Eimeria within the Marmotini tribe.