The Republic was briefly occupied by the Austrian forces in 1800, but Napoleon soon returned with his army. A new Constitution was published in 1801, establishing institutions more similar to those of the previous Genoan Republic, with a Doge who was president of a Senate.
In June 1805, the area was directly annexed by France as the départements of the Apennins, Gênes and Montenotte. After the fall of Napoleon in 1814 the republic was briefly restored between 28 April and 28 July. Following the Congress of Vienna it was awarded to the Kingdom of Sardinia, and annexed on 3 January 1815. The Ligurian Republic used the traditional Genoese flag, a red cross on a white background.