Clinician and researchers continue to encounter significant challenges in treating women dually diagnosed with posttraumatic stress disorder (PTSD) and a substance use disorder (SUD). This study examined the predictive value of dissociation on treatment outcome and determined whether cognitive-behavioral therapy (CBT) treatment interventions are effective in reducing reported dissociation in urban women dually diagnosed with PTSD and SUD. A secondary aim examined the relationship between dissociation and therapeutic alliance. Analyses also tested for therapist effects. Women were randomly assigned to either a standard relapse prevention or integrated Seeking Safety treatment intervention group. These intervention groups were compared to a non-randomized standard community care control group. Results revealed that CBT treatment intervention is effective in reducing reported dissociation scores. In addition when compared pair-wise, it was found that some therapists were more effective in reducing reported dissociation scores. Baseline dissociation scores did not predict treatment outcome and there was no significant relationship between dissociation and therapeutic alliance.