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Research has shown that family functioning has been positively associated with physical activity and dietary intake, both of which are obesity-related risk factors. The most widely practiced methodological approach to assessing this construct in empirical studies relies on either parent or adolescent report. Yet, discrepancy in parent and adolescent report of family functioning may provide a fuller understanding of the effects of this construct on obesity-related health outcomes. This is especially important among Hispanics, a population that suffers from disproportionately high rates of obesity and its health-related consequences. The purpose of this study was to examine whether, and to what extent, parent-adolescent discrepancies in family functioning are associated with physical activity, and fruit and vegetable and added sugar intake. We estimated discrepancy scores between parents and adolescents (n = 280 dyads) in family functioning. Then, using structural equation modeling, we tested the effect of family functioning discrepancy on adolescent reports of physical activity, fruits and vegetables intake, and added sugar intake. After controlling for adolescent’s gender and BMI, family functioning discrepancy was significantly associated with reduced physical activity (β = −.14*, 95% CI ([−.26, −.05]) and fruits and vegetables intake (β = −.22*, 95% CI [−.38, −.09]) such that the larger the discrepancy between parent and youth reported family functioning, the fewer days of adolescent physical activity and the poorer the fruits and vegetables intake. Our findings provide insight for the role of the family in Hispanic adolescent health outcomes and rationale for capturing rich data to better understand that role.