Genetic makers play a critical role in coronary artery disease (CAD) susceptibility. This study investigates the association between angiotensin-converting enzyme (ACE) insertion/deletion (I/D) and endothelial nitric oxide synthase (eNOS)-786 T > C polymorphism with CAD in the Pashtun ethnic population of Khyber Pakhtunkhwa, Pakistan. This case–control study was conducted on 1000 individuals, including 500 CAD patients and 500 healthy controls. Genotyping of ACE I/D and eNOS-786 polymorphisms was performed using polymerase chain reaction and polymerase chain reaction-restriction fragment length polymorphism techniques. The association of polymorphisms with CAD risk was analyzed using logistic regression to determine odds ratios (ORs) with 95% confidence intervals (CIs). The ACE deletion (D) allele was significantly more frequent in CAD patients than in controls (OR = 4.76, 95% CI: 3.21–7.08, P < .001), indicating a strong genetic predisposition. Similarly, individuals with the ACE DD genotype had a markedly higher risk of CAD (OR = 6.42, 95% CI: 3.89–10.59, P < .001) compared to individuals with II genotype. In contrast, no significant association was observed between eNOS-786 polymorphism and CAD risk (OR = 1.08, 95% CI: 0.72–1.61, P = .98). The ACE I/D polymorphism, particularly the DD genotype, is strongly associated with an increased risk of CAD in the Pashtun population, while eNOS-786 polymorphism does not appear to be a significant risk factor. These findings underscore the importance of genetic screening for early risk assessment and developing intervention therapies according to genetic make-up of individuals for more effective disease prevention.