Although the comorbidity between borderline personality disorder (BPD) and substance abuse is well established, there are few longitudinal studies that have examined its developmental origins or whether the comorbidity is due to common genetic or environmental risk factors. To fill this gap, we used a large sample of female adolescent twins (N = 1,280) to examine the developmental course, reciprocal influences, and the genetic and environmental factors underlying the co-occurrence of BPD traits and substance use from age 14 to 18. Rank-order stability was moderate to high for both BPD traits (r = .58) and substance use (r = .51), whereas mean levels of substance use increased substantially from age 14 to 18 (d = 0.77) and BPD traits showed a small decline (d = -0.21). BPD traits and substance use exhibited concurrent and prospective associations; however, the longitudinal associations dropped to nonsignificance after accounting for the temporal stability of each trait. Twin analyses revealed that shared environmental factors accounted for the association between BPD traits and substance use at age 14, but genetic factors accounted for the association at age 18. These results indicate that, at least in adolescence, the comorbidity between BPD traits and substance use is a consequence of common risk factors rather than due to one being a casual antecedent of the other.