In 51 to 50 BC, he was governor of Syria, where he was effective but alienated the army by taking too much personal credit for the repulse of the Parthians. In 49, after Caesar's Civil War broke out, Bibulus aligned himself with Pompey and was in charge of the fleet tasked with preventing Caesar from shipping his army across the Adriatic. He failed to do so and subsequently failed to effectively cut off Caesar's supplies. On blockade duty in 48 BC, he fell ill and died.