Toxoplasma (T.) gondii and Neospora (N.) caninum are two significant abortifacient apicomplexan protozoa causing severe economic losses in livestock farming. This study was designed to investigate the serological status of T. gondii and N. caninum in sheep and goats across the Southeastern Anatolia Region of Türkiye, including some provinces bordering Syria and Iraq. Totally, 906 serum samples collected from female sheep (n=510) and goats (n=396) were investigated for specific antibodies against these protozoa by recombinant TgSAG2 and NcSAG1 protein-based indirect ELISA (iELISA). The individual seroprevalence of T. gondii and N. caninum in sheep was determined as 32.6 and 3.1%, respectively, while the seroprevalence of infection with both species was 33.1%. On the other hand, T. gondii and N. caninum seroprevalence in goats were 32.1 and 20.2%, respectively, while the total seroprevalence of infection with both species was 39.4%. The highest seroprevalence values for T. gondii (P<0.05) and N. caninum (P>0.05) were determined in sheep from Diyarbakır and Mardin provinces, respectively, while in goats, higher seroprevalence values for both protozoa were determined in Diyarbakır province compared to other provinces (P<0.05). Statistical analyses revealed that seroprevalence values varying between provinces were significant (P<0.05), except for ovine neosporosis (P>0.05) and when seroprevalence values between animal species were compared, caprine neosporosis was statistically significantly higher (P<0.05). The fact that 35.9% of the small ruminants enrolled in the study had been exposed to abortive apicomplexan protozoa during their lives is a serious concern, given the zoonotic aspects of these protozoa and the economic damage they can cause.