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Hypertension is an emerging public health problem in Bhutan due to epidemiological and nutritional transitions in the last two decades. This study aimed to quantify risk factors of hypertension in Bhutan using nationally representative data. This was a secondary data analysis of a nationally representative World Health Organization Non-Communicable Disease STEP-wise Survey of Bhutan carried out in 2019. Multivariable logistic regression analysis was conducted to identify the risk factors of hypertension in the population 40-69 years age group. The Bayesian network (BN) analysed the influencing factors on the prevalence of hypertension. Of the 2,574 individuals aged 40-69 years sampled, 56.8% were women. The prevalence of hypertension was 44.3% (1,140). In multivariable logistic regression, participants in 55-59 and 60-64 years were 44% (adjusted odds ratio [AOR] = 1.44; 95% confidence interval [CI] 1.06, 2.14) and 65% (AOR = 1.65; 95% CI 1.17, 2.42) higher odds of developing hypertension than 40-44 years old. Compared to non-formal education, certificate and bachelor, and year 12 educated were 77% (AOR = 1.77; 95% CI 1.01, 3.12) and 54% (AOR = 1.54; 95% CI 1.02, 2.32) odds of reporting hypertension. The higher wealth index had lower odds of hypertension than those in the lower wealth index. Alcohol use was associated with developing hypertension (AOR = 1.73; 95% CI 1.39, 2.15) compared to non-drinkers. Those who chewed betel quid were 38% (AOR = 0.62; 95% CI 0.50, 0.76) less odds of reporting hypertension than those who did not chew betel quid. Individuals with obesity (AOR = 2.39; 95% CI 1.84, 3.12) and overweight (AOR = 1.44; 95% CI 1.04, 1.98) had more than twice and 44% higher odds of developing hypertension compared to those with normal body mass index (BMI). Borderline (AOR = 2.0; 95% CI 1.05, 3.81) and high cholesterol levels (AOR = 1.84; 95% CI 1.32, 2.57) were associated with an increased odds of hypertension compared to normal blood cholesterol levels. The conditional probability of hypertension using BN showed that obese and border blood cholesterol was associated with an increased odds of hypertension. While use alcohol use and chewing betel quid lowered the odds of hypertension. These findings highlight the need for targeted hypertension prevention strategies that address both behavioural and socioeconomic factors such as older age, alcohol use, pre-obesity and obesity, and high cholesterol levels. Therefore, the Ministry of Health, Bhutan should implement a comprehensive prevention and management program that include both clinical care and non-pharmacological strategies such as promoting healthy lifestyles, maintaining optimal body weight, and conducting regular screenings for hypertension and related conditions like high cholesterol.