Merlin rallied to Napoleon during the Hundred Days, and seized the fort of Vincennes on 20 March 1815. He then organized, and became major of the new 2nd regiment of Chasseurs à Cheval of the Imperial Guard. On 13 June 1815, he was given command of the 2nd brigade in Subervie's 5th Cavalry Division of the Army of the North. During the Waterloo campaign, this formation fought on the French left at Ligny and in the defence of Plancenoit at the battle of Waterloo.