This 6-year community study examined how discrepancies in mothers’ and adolescents’ perceptions of their relationship were longitudinally associated with adolescent internalizing symptoms, and vice versa. 497 adolescents (57% boys, Mage T1 = 13.03, SDage = 0.46) and their mothers reported in 6 annual waves on conflict and warmth in the mother-adolescent relationship and adolescents reported on their depressive and Generalized Anxiety Disorder (GAD) symptoms. Latent Congruence Models suggested that both adolescent depressive and GAD symptoms significantly predicted higher levels of conflict as well as stronger discrepancies in perceptions of conflict 1-year later. In turn, higher levels of conflict significantly predicted both adolescent depressive and GAD symptoms 1-year later. For warmth, lower levels significantly predicted adolescent depressive symptoms 1-year later. Concluding, these findings suggest (1) more systematic evidence for longitudinal associations between conflict than warmth in the mother-adolescent relationship and adolescent internalizing symptoms; (2) support for a transactional model, including support for both interpersonal scar or symptom-driven effects (concerning both levels of and mother-adolescent discrepancies in conflict) and interpersonal risk or relationship-driven effects (concerning levels of both conflict and warmth); (3) longitudinal effects from adolescent internalizing symptoms to mother-adolescent discrepancies, but not vice versa; and (4) strong consistency in patterns of findings across both adolescent depressive and GAD symptoms, with few differential longitudinal associations with aspects of mother-adolescent relationship quality. Thereby, this study provides a more nuanced understanding of the direction of effects between adolescent internalizing symptoms and both levels of and discrepancies in mothers’ and adolescents’ perceptions of their relationship.