Klein was appointed general of division in 1799 and crossed the Rhine at Kehl in Jean-Baptiste Jourdans Army of the Danube. He commanded the right flank of the Advance Guard, under command of François Joseph Lefebvre. His command included the 4th and 5th Hussar Regiments, the 17th Dragoons, the 1st "Chasseurs à cheval", a light horse regiment, two companies of horse artillery, two of foot artillery, and a company of sappers. At the Battle of Ostrach, Klein's cavalry helped to secure the village of Hosskirch, a strategically important forward post, prior to the general engagement. After the French losses at Ostrach and the subsequent Battle of Stockach, Jourdan ordered a general withdrawal to the Black Forest. The reserve cavalry and most of Klein's division crossed the mountains and quartered near Offenburg, where their horses could find better forage. Despite the organized withdrawal and the relatively secure positions on the western side of the Black Forest, the army was in shambles. Jourdan placed his chief of staff Jean Augustin Ernouf in provisional command and went to Paris to complain about the state of his army, its equipment and its provisions. Discipline in the ranks disintegrated. Most of the divisional generals left their posts, except for Pierre Marie Barthélemy Ferino, Joseph Souham, Dominique Vandamme and Klein. In May, Andre Massena received overall command of both the Army of the Danube and the Army of Helvetia; Klein's column joined Massena near Zurich.