The distinction between low-anxious primary versus high-anxious secondary psychopathy is well-established among incarcerated adults and adolescents. However, no studies have used a prospective longitudinal approach to explore whether primary versus secondary psychopathy variants have different rates of alcohol and marijuana use across adolescence, and what mechanisms account for these differences. The sample was 1,170 male adolescents who had interacted with the justice system, with data collected as part of the Pathways to Desistance project. We used interviewer assessments of psychopathy and self-reported anxiety at baseline to identify primary and secondary psychopathy subgroups. We explored subgroup differences via self-reported measures of psychopathic traits and anxiety, aggression, depression, and posttraumatic stress disorder symptoms at baseline and a 6-month follow-up. Finally, we tested whether groups had different trajectories of alcohol and marijuana use over 4 years, and whether poor impulse control or anxiety mediated these differences. Latent profile analysis identified four groups: low-anxious primary psychopathy, high-anxious secondary psychopathy, anxious only, and low risk. The secondary group had similar levels of aggression and psychopathy to the primary group, but more depression, anxiety, and posttraumatic stress symptoms. The primary and secondary psychopathy variants did not differ in rates of alcohol or marijuana use across adolescence, but alcohol use among secondary variants was specifically mediated via poor impulse control. The findings establish two psychopathy groups that differ meaningfully in their internalizing psychopathology and pathways to alcohol use.