Background: Research on the associations between walking and cycling with obesity-related phenotypes is growing but relies mostly on the use of BMI. The purpose of this study was to analyze associations of walking and cycling behaviors assessed separately with various obesity markers in French adults. Methods: In 12,776 adult participants (71.3% women) of the on-going NutriNet Santé web-cohort, we assessed by self-report past-month walking and cycling (for commuting, errands and leisure), and obesity measures were taken during a visit at a clinical center (weight, height, waist circumference, and percent body fat by bioimpedance). Results: In analyses not taking into account other types of physical activity (household, leisure), walking more than 2.5 h/week was associated in women with lower weight (-1.8 kg), waist circumference (-1.7 cm) and percent body fat (-1.1%) (all p < 0.001). Cycling more than 1.5 h/week was associated in men and women with lower weight (-4.3 and -1.4 kg, respectively), waist circumference (-4.4 and -2.1 cm, respectively), and percent body fat (-2.5 and -1.9 % respectively) (all p < 0.001). Results were unaltered when analyses were further adjusted on household and leisure physical activity. Conclusion: These results show important differences between walking and cycling in their association with obesity markers in men and women. These findings provide some evidence for the need to consider separately walking and cycling when designing public health measures for prevention of obesity in adults.