Background <p><i>Theileria</i> species is an important tickborne pathogen of sheep and goats globally. This study was performed in western Saudi Arabia to investigate the prevalence, associated risk factors, and phylogenetic analysis of <i>Theileria ovis</i> (<i>T. ovis)</i> in sheep and goats.</p> Methods <p>A total of 300 blood samples, 190 from sheep and 110 from goats, were collected. The investigation was performed using PCR targeting the small subunit ribosomal RNA (<i>ssu rRNA</i>) gene, in addition to genetic characterization.</p> Results <p>The proportion of goats and sheep testing positive was variable ranging from 9.1 to 13.2%. The total prevalence of <i>T. ovis</i> was found to be 9.1% in goats and 13.2% in sheep. The enrolled sheep and goats were confirmed to be infected with <i>T. ovis</i> by sequencing the partial <i>ssu rRNA</i> gene, and a similar genotype was identified. Age, housing, sex, and tick infestation factors were significantly associated with the infection (<i>p &lt;</i> 0.05). Multivariable model analysis indicated that <i>T. ovis</i> infection was 4.6, 0.4, 3.1, and 8.2 times higher in ages <i>&gt;</i> 1 year, females, closed housing, and tick infestation, respectively. Phylogenetic analysis and high nucleotide identities revealed similar genotypes of <i>T. ovis</i> exist in the field, and were close to Turkish <i>T. ovis</i> (OM066225, a goat strain).</p> Conclusions <p>We reported a low to relatively moderate molecular prevalence of <i>T. ovis</i> in goats and sheep, respectively, from the western region. However, it is recommended to adopt control measures to reduce <i>T. ovis</i> infection in small ruminants in this area.</p>