Her second marriage, in December 1197, was to Count Bernard IV of Comminges, and at the insistence of her father, Marie renounced to her rights over Montpellier in favor of her eldest half-brother William (IX), son of Agnes.
From her marriage with Bernard IV, Marie had two daughters, Mathilde (by marriage Viscountess de la Barthe) and Petronille (by marriage Countess of Astarac).
The marriage was, however, notoriously polygamous (Bernard IV had two other living wives) and was finally annulled (some say on Marie's insistence, some say on that of King Peter II of Aragon) in 1201. With this annulment, Marie was once more heir to Montpellier, but her father never recognized her and openly acknowledge his son William IX as his heir.