According to the first historical data, the earliest evidence of human settlements goes back to 500 B.C.; they mainly refer to people of Etruscan origin or other stationary or semi-nomadic civilizations which were later incorporated to the Roman dominion.
Built by Longobards on the ruins of previous fortifications, the Castle dates back to 500 A.D.
When the Franks defeated the Longobardic armies in 509 A.D., the castle was partly destroyed and then rebuilt.
Alberto della Scala, lord of Verona, modified the Statutes of Verona in 1277. This documents established that any castle or fortress belonging to the town territory had to be regulated by the central power. An exception was made for the castle of Malcesine and six other buildings which were confiscated and put under the direct control of the lord.
The new lords modified the old building and since then, the castle was named "Scaligero" (Scaliger, from della Scala).
Charles IV, king of Bohemia, granted Mastino II della Scala the captaincy on the Lake and the right to appoint or remove protectors and officials in 1351. This marked the beginning of Garda Federation and the Lake Captaincy (Gardesana dell'Acqua) which lasted till the Italian Republic was constituted (1802).
Gardesana dell'Acqua was a federation of 10 municipalities endowed with wide authonomy. It was made up of three colonelcy: the upper one included Malcesine, Brenzone and Pai; the middle one Torri, Albisano, Garda and Costermano while the lower covered the territory of Bardolino, Cisano and Lazise. They elected 18 councilors (three of them living in Malcesine) and a mayor, usually residing in Torri, where the assemblies chaired by the Lake Captain were held.
The Captain had the duty of defending and monitoring the federal territory as well as carring out ordinary tasks of law and order.
The Captain lived in Malcesine, the closest town to the border, and in order to give him a suitable location, in 1618 the Municipality of Verona acquired the Scaliger "casamentum" building which is now called Palazzo dei Capitani.
The thriving development of the federation did not affected the different municipalities. As a result, the municipality of Malcesine kept its own rights, among whom the most relevant was the establishment of three councils: "consiglio Piccolo" dealing with standard tasks, "consiglio Grande" handling essential issues and "consiglio Maggiore", whose members were the head of the families, taking care of extraordinary questions.
The Gardesana dell'Acqua, in its 450 years of existence, has been the scene of many battles: the best known was the one between Venice and the House of Visconti of Milan during which some Venetian galleys were carried from the river Adige into Lake Garda.
The House of Visconti supplanted the House of Scaliger in 1387. Then, in 1405 it was the Doge of Venice's turn to succeed.
When the League of Cambrai attacked Venice, Malcesine went under the emperor Maximilian I dominion from 1508 to 1516. Then, the Venetian power was restored again.
When Napoleon declared war on Austria in 1796 to gain control over Lombardy and the rest of Northern Italy, many French and Austrian troops were sent to Malcesine. But, even if the neutral control of Venice no longer existed, the administrative structure of both the Municipality and the Gardesana dell'Acqua remained unaltered during the French domination and later on, under the Austrian authority which started in 1798.
On February 18, 1801, following the Treaty of Luneville, the Cisalpine Republic annexed Malcesine.
When the Italian Napoleonic Republic was founded in 1802, the federation, the captaincy and the Consiglio maggiore where all suppressed and replaced by town councils.
With Napoleon's fall, Malcesine was annexed to the Kindom of Lombardy and Venetia.
Malcesine parlty experienced the hardships related to the Italian Unification. The town suffered the Piedmontese occupation for a short period following the Battle of Goito in 1848, and then, it went under the Austrian dominion until it became part of the Kingdom of Italy in 1866.