The present study: (1) examined relations between parent psychopathology and adolescent internalizing problems, externalizing problems, and substance use in substance-abusing families; and (2) tested family functioning problems as mediators of these relations. Structural equation modeling was used to estimate the independent effects of parent psychopathology and family functioning problems by parent gender. Participants included 242 parents in treatment for substance abuse and/or dependence and 59 of their coparents (16.9% in treatment for substance-abuse/dependence) from middle income households (SES: M = 4.7; SD = 2.1). Ratings were obtained for 325 adolescents (48% female; 27.8% non-Caucasian) between the ages of 10 and 18 years (M = 13.5 years; SD = 2.5 years). Parent psychopathology, family functioning problems, and adolescent problems were assessed with parent and coparent ratings on the Symptom Checklist (SCL-90)/Brief Symptom Inventory (BSI), the Family Relationship Measure, and the Child Behavior Checklist, respectively. Results indicated that maternal psychopathology was directly related to adolescent internalizing problems and substance use, but maternal perceptions of family functioning problems failed to mediate relations between maternal psychopathology and adolescent problems. By contrast, paternal perceptions of family functioning problems uniquely mediated relations between paternal psychopathology and adolescent externalizing problems. Findings underscore the importance of examining how mothers and fathers may differentially impact adolescent problems in substance-abusing families.