The city of Lindau became a Free Imperial City in the 13th century; it was directly subordinate to the emperor. The rural areas around Lindau were the property of monasteries or tiny counties, that rose and fell in the region. When Napoleon gained influence in the area, all these entities were dissolved in the German Mediatisation. Lindau fell to Bavaria.
The district of Lindau was established in 1938. After the Second World War it became part of the French zone of occupation, while the rest of Bavaria was under American occupation. In 1955 the district was reincorporated into Bavaria. The city of Lindau, which had been an urban district, became a part of the rural district in 1972.