This research examined the relationship between parenting practices and adolescent conduct problems and the mediation of these relationships by two parent-adolescent relationship variables, conflict and psychological autonomy. Autoregressive latent trajectory (ALT) analyses were used to assess relationships over time between parent practices and adolescent conduct problems. Participants were 2,453 students recruited from 7 public middle schools and assessed 5 times between fall of 6th and 9th grades on the following measures: Parent Monitoring; Parent Knowledge; adolescent Psychological Autonomy; parent-adolescent Conflict; and adolescent Conduct Problems. Adolescent Conduct Problems and parenting practices were associated in both cross-sectional and prospective analyses. In time-lagged autoregressive modeling as a part of ALT analyses, adolescent Conduct Problems and parenting practices were reciprocally related from Time 1 to Time 2, but there after only Parent Monitoring was consistently associated with adolescent Conduct Problems over time. Adolescent Psychological Autonomy positively mediated the relationships between adolescent Conduct Problems and Parent Monitoring, but not the relationship between Parental Knowledge and Conduct Problems; while Conflict partially mediated the relationships between the slope of Conduct Problems and the slopes of both parenting behaviors and the relationship between the slopes of Conduct Problems and Psychological Autonomy. The findings provide evidence of reciprocal relationships between Conduct Problems and parenting behaviors and parent-teen relationship variables. Mediational analyses indicated relationships with Conduct Problems unmediated by Autonomy and partially mediated by Conflict. The findings provide support for the hypothesis that associations over time between parenting practices and adolescent Conduct Problems depend in part on the parent-adolescent relationship. (Contains 4 tables and 3 figures.)