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Objective Coronary artery disease (CAD) is the principal cause of mortality and morbidity worldwide. Studies have provided controversial results regarding whether variations in the proprotein convertase subtilisin/kexin type 9 gene ( PCSK9 ) are risk factors for CAD. In this study, we evaluated the risk factors associated with PSCK9 genotypes and CAD in the Taiwanese population. Methods A total of 501 patients diagnosed with CAD by angiography and 334 CAD-free controls were recruited. Two single nucleotide polymorphisms of PSCK9 (rs505151 and rs529787) were genotyped. Results The prevalence of a positive family history for CAD was significantly higher in individuals carrying the AG + GG genotype of the PSCK9 rs505151 polymorphism. Among CAD patients with a positive family history, the prevalence of diabetes mellitus was significantly higher in those carrying the AG + GG genotype of the PSCK9 rs505151 polymorphism (73.3%) than in those carrying the AA genotype (39.2%). Conclusion In CAD patients, the AG genotype of PSCK9 rs505151 is associated with diabetes and a positive family history of CAD.