Annecy has one of the most ancient human settlements in the Northern Alps, with its history as a coastal village dating back to 3,100 BC. Traces of the dwellings of the Gallo-Roman tribe called Boutae have been found nearby Annecy (50 B.C.). The approximately 2,000 inhabitants of this period are credited with forming a triangular settlement, which emphasized the importance of the roads entering the junction of town. Points led to Faverges (Casuaria), Aix-les-Bains (Aquae) and Geneva.
The Roman Emperor Anicius Olybrius built himself a villa on the lake called Anneciacum hence the town’s name.
Some time after the dispersion of the Boutae population, a medieval town developed on the banks of the Thiou. The fortifications of the town later became a castle, Annecy-le-Neuf, in 1107. The town saw a rapid expansion in the 10th century, when it became the capital of the county of Geneva, and residence of the Count of Geneva who was driven out of his original capital following conflicts with his bishops. The town castle was the royal residence until the Geneva family line came to an end in 1394, following the death Robert of Geneva, the antipope of Avignon known under the name of Clément VII. As a result, Annecy became integrated into the House of Savoie in 1401 under the authority of Amadeus VII, the first Duke of Savoie. The former Genevan capital endured a series of severe fires that destroyed the greatest part of the city in 1412 and again in 1448. Amadeus VII is credited with reconstructing the city. In 1444, it was set up by the Princes of Savoie as the capital of a region covering the possessions of the Genevois, Faucigny and Beaufortain.
With the advance of Calvinism in 1535, it became a center for the Counter-Reformation. The Reformation drove out the Bishop of Geneva from its town and the bishop's see of Geneva was transferred here. It suppressed in 1801, though restored in 1822. Annecy soon became known as the ‘Rome of the Alps’. It was during this time that some of the city’s most appealing monuments were constructed such Saint Peter’s Cathedral and the Notre-Dame de Liesse church tower. St. Francis of Sales was born at the castle of Sales, close by, in 1567. He was bishop of Annecy from 1602 to 1622. In 1728, 16-year-old Jean-Jacques Rousseau took refuge in the city. In the courtyard of the bishop's palace, a bust commemorates the place where Jean-Jacques Rousseau met Madame de Warens.
During the French Revolution, the Savoy region was conquered by France and Annecy became attached to the département of Mont Blanc. It opened the region to industrial redevelopment and stimulated economic growth. Factories were set up, powered by the hydraulic force of the Thiou River. After the Bourbon Restoration in 1815, Annecy was returned to the House of Savoy. When Savoy was annexed by France in 1860, Annecy became the capital of the new département of Haute-Savoie. The Thiou River played a key economic role as early as the Middle Ages, thanks to its regular rate of flow that supplied the required hydraulic energy for the development of the craft industry in the region. In 1870, when he was the Highway Department engineer, Sadi Carnot completed a system of gates to regulate the flow of the Thiou, raise the level of the lake, and thus facilitate the navigation of the merchant ships so vital to the economy of the city. In 1887, Sadi Carnot became President of the French Republic!