Background: Hypertension has gained global significance and risk of cardiovascular disease, and adiposity is the most important of the conditions associated with and considered responsible for hypertension in children. Therefore, the present study aimed to determine whether indices of adiposity independently predicted blood pressure at multiple points in gender-specific groups. Methods: This was a cross-sectional study involving 10 randomly selected primary schools within the Ellisras Longitudinal Study, and involved 1816 adolescents (876 girls and 940 boys) aged 8 to 17 years. All the anthropometric indices and blood pressures (BP) were examined according to the International Society for the Advancement of Kinanthropometry protocol. Results: In an adjusted linear quantile regression analysis of boys, waist circumference (WC) was associated with BP across all multiple points of systolic blood pressure (SBP). Furthermore, the triceps skinfold site was associated with high SBP. In girls, body mass index (BMI) was significantly associated with SBP after adjustment for potential confounders. Other anthropometric indices of adiposity, including WC, biceps, and triceps skinfold sites were not associated with SBP. Conclusions: The results of the present study suggest that in black South African children, variables such as WC and triceps skinfold site may provide stronger explanatory capacity to SBP variance and systolic hypertension risk in boys than other adiposity indices; whereas in girls, only WC and BMI predict diastolic blood pressure (DBP) and SBP, respectively.