Globally, adolescents in sub-Saharan Africa are the youth most affected by HIV. Parent-adolescent relationships can be protective in child and adolescent development and may be implicated in lowered adolescent HIV sexual risk. However, the importance of parental and adolescent perceptions of their relationship and assessing the implications of family functioning in adolescents' risk for HIV or other sexually transmitted infections are not well established in the research literature. This dyadic study simultaneously assessed both parents' and adolescents' perceptions of family functioning and their relationships with adolescent sexual behaviors in Botswana. Seventy-two parent-adolescent dyads completed audio computer-assisted self-interview surveys. Surveys, independently completed by parents and their adolescent, assessed multiple indicators of their relationship and is the first such study in Botswana to collect the perspectives of both the parents and their adolescents. The results highlight significantly discrepant views of their relationships and revealed that the magnitude of those discrepancies was associated with greater adolescent HIV sexual risk behavior across multiple measures of family relationships. Parents' inaccurate perceptions of their adolescents' sexual activity were also associated with greater adolescent sexual risk. These findings elucidate the importance of improving parent-adolescent communications and relationships, which may subsequently assist in lowering adolescents' sexual risk for HIV and other negative sexual health outcomes.