Anaplasmosis is a major tick-borne infectious disease affecting small ruminants, leading to significant economic losses due to decreased productivity and, in some cases, mortality. This study aimed to determine the molecular prevalence of Anaplasma ovis and Anaplasma phagocytophilum infections in goats raised in Siirt province, Türkiye, and to genetically characterize the detected isolates based on the major surface protein 4 (MSP4) gene region. A total of 250 randomly selected apparently healthy goats were sampled between July and September 2025. The overall molecular prevalence of A. ovis was found to be 52% (130/250), while A. phagocytophilum was not detected in any of the screened animals. Significant associations were observed between A. ovis positivity and age, sex, breed, and sampling districts within Siirt province (p < 0.05), with the highest infection rates observed in goats older than 1 year (63.6%), female goats (58.2%), Damascus goats (66.7%), and goats sampled from the Kurtalan district (87.1%). Sequencing analysis of selected samples yielded high-quality MSP4 gene sequences showing 100% nucleotide identity with reference A. ovis isolates from Iran, Italy, Pakistan, Sudan, Tunisia, and Türkiye. Phylogenetic analysis supported species-level identification by grouping the study isolates with reference A. ovis sequences; however, broader evolutionary inferences should be interpreted cautiously due to the short fragment length and limited number of sequenced isolates. The findings of this study provide updated molecular epidemiological data on caprine anaplasmosis in southeastern Türkiye and highlight the utility of the MSP4 gene as a reliable molecular marker for species identification and phylogenetic analysis. These results contribute to a better understanding of the epidemiology of A. ovis and may support the development of effective control strategies in small ruminant production systems.