Waterpipe smoking is a form of tobacco use that causes nicotine/tobacco dependence and has become a global health problem. In this study, the association of rs16969968 SNP in the CHRNA5 gene with waterpipe dependence was investigated. A total of 386 men and women who used a waterpipe to smoke tobacco were recruited and divided into less dependent and more dependent smokers based on their score on the Lebanon Waterpipe Dependence Scale (LWDS). Results showed a significant difference in the distribution of GG, GA, and AA genotypes by waterpipe dependence status (p < .001). The more dependent group showed a higher frequency of the AA genotype than the less dependent smokers' group (38% vs. 23%, respectively). In addition, the more dependent smokers exhibited more A allele than less dependent smokers (53% vs. 37% respectively, p < .001). In conclusion, there is an association between the rs16969968 SNP and waterpipe dependence as assessed by the LWDS.