One of the areas in Türkiye where animal husbandry is practiced extensively is the Eastern Anatolia Region. In the province of Van, which belongs to this region, depending on the sociocultural factors of the people, animal husbandry is carried out, especially in the form of small ruminant breeding. One of the most commonly reported intracellular tick-borne illnesses, Anaplasma ovis, infects ruminants worldwide and results in significant financial losses. The purpose of this study was to report the prevalence and phylogeny of this pathogen in goats that were obtained from Gevas, Van Province, Türkiye, via the msp4 gene. Blood samples were taken from the vena jugularis to the EDTA tubes from 205 randomly selected goats (apparently healthy) between April and June 2022. Using a pair of primers called MSP45/MSP43, the msp4 gene (major surface protein 4) of A. ovis was amplified from all the DNA samples via PCR. A total of 146 (71.2%) of the 205 samples amplified a fragment of 852 bp that was unique to the A. ovis msp4 gene. Sanger sequencing verified the presence of incomplete msp4 gene sequences, which were subsequently added to GenBank (PP625125–PP625128). None of the studied epidemiological characteristics (sex, age, infertility problem, history of abortion, or shelter conditions) were associated (P > 0.05) with A. ovis infection in the enrolled goats. Furthermore, there were variations in the prevalence of A. ovis in goats among the sampling sites. The analysis of the amplified partial msp4 sequence of A. ovis indicated that this gene is highly conserved, since all four sequences are phylogenetically closely related to each other and to the msp4 sequences amplified from other countries. The detection and phylogenetic analysis of A. ovis in this study have contributed to the existing knowledge of the parasite and provided valuable data on caprine anaplasmosis. Additionally, this research highlights the urgent need for further investigation and the implementation of targeted control measures in the region.