Background Endothelial dysfunction is one of the most important early indicators of atherosclerosis in obstructive sleep apnea (OSA) patients. Endothelial cell specific molecules-1 (ESM-1), which is a novel endothelial dysfunction marker that may be linked to cardiovascular disease. We investigated to assess whether circulating ESM-1 levels are correlated with the presence of coronary artery disease (CAD) in patients with OSA. Methods We performed a cross-sectional study in 228 Chinese OSA subjects, including 185 patients with OSA and 43 controls. The Gensini stenosis scoring system was used to assess the severity of CAD. Circulating ESM-1 levels were measured by Human Magnetic Luminex Screening Assay. The associations between circulating ESM-1 levels and CAD were determined by multivariate logistic regression analysis. The association between ESM-1 levels and Gensini scores was determined by multivariate linear regression analysis. Results CAD patients had significantly higher circulating ESM-1 levels compared with non-CAD patients (1279.01[918.52-1770.71] pg/ml vs 585.46[423.61-812.56] pg/ml, P < 0.001). After adjusting for confounding factors, we found that circulating ESM-1 levels were an independent risk factor for CAD (OR = 1.633/100 pg ESM-1, 95%CI =1.179-2.262, P = 0.003), while circulating ESM-1 levels have no significant correlation with the Gensini score. Furthermore, circulating ESM-1 showed higher discriminatory accuracy in predicting the presence of OSA (AUC:0.910). Conclusions Circulating ESM-1 might function as a useful biomarker for monitoring the development and progression of CAD in OSA patients.