Caprine piroplasmosis is caused by various species belonging to Babesia and Theileria genera and it is a major pathological condition affecting goats globally, particularly in tropical and subtropical regions, including Türkiye. In endemic areas, these infections cause huge losses and are major threat to the sustainability of goat farming. Despite their impact, data on the molecular prevalence and genetic diversity of these pathogens in Türkiye remain limited. This study aimed to determine the molecular prevalence of caprine piroplasm agents in 400 goats sampled from nine provinces of Southeastern Anatolia, a key goat-farming region of Türkiye, and to perform phylogenetic characterization of the detected parasite species. Genomic DNA extracted from blood samples was initially screened using nested PCR targeting the 18S rRNA gene, followed by species-specific PCR to identify Babesia ovis, Babesia aktasi, Theileria ovis, Theileria luwenshuni, Theileria uilenbergi, and Theileria lestoquardi. Overall, 10.3% (41/400) of goats were infected with at least one piroplasm species. Babesia ovis (9.5%, 38/400) and T. ovis (3.8%, 15/400) were identified as the main causative agents in the region, with most T. ovis infections occurring as co-infections with B. ovis (3%, 12/400). None of the goats was found to be infected with B. aktasi, T. uilenbergi, T. luwenshuni and T. lestoquardi. Statistical analyses showed significant associations of B. ovis infections with province and goat breed (p < 0.05), while T. ovis infections were significantly associated with province, age, and goat breed (p < 0.05). Both parasites were confirmed by DNA sequencing and phylogenetic analysis revealed their homology with sequences submitted previously from Türkiye and neighboring countries. These findings underscore the importance of identifying carrier animals to better elucidate the epidemiology of caprine piroplasmosis and develop effective control strategies to mitigate its spread; therefore, continuous surveillance and targeted management strategies are essential to minimize the impact of these tick-borne pathogens on goat farming in Türkiye.