A comorbid posttraumatic stress disorder (PTSD) aggravates symptoms, course of illness and social functioning of persons with borderline personality disorder (BPD). However, it is largely unclear how this effect is mediated. In 60 women with BPD of whom 23 had a comorbid current PTSD we investigated whether dysfunctional explicit and implicit emotions were associated with a comorbid PTSD. Shame and guilt proneness, anxiety, anger–hostility, and general psychopathology were assessed by self-report measures. Implicit anxiety-related self-concept was measured using the Implicit Association Test. Self-reported guilt proneness and general psychopathology, but not shame proneness or trait anxiety, were significantly higher in women with BPD and PTSD than in women with BPD alone. A comorbid PTSD was associated with a more anxiety-prone (relative to shame-prone) implicit self-concept as assessed by the Implicit Association Test. Self-reported guilt proneness and implicit anxiety may mediate the negative impact of comorbid PTSD on women with BPD.