Perona as founded by the bishop of Ösel-Wiek ca. 1251, suffered heavily under pressure of the concurrent town, and was finally destroyed ca. 1600. Another town, Embeke (later German: Neu-Pernau, Estonian: Uus-Pärnu) was founded by the Livonian Order, who began building an Ordensburg nearby in 1265. The latter town, then known by the German name of Pernau, was a member of the Hanseatic League and an important ice-free harbor for Livonia. The Polish-Lithuanian Commonwealth took control of town between 1560–1617; the Poles and Lithuanians fought the Swedes nearby in 1609. Sweden took control of the town during the 16th century Livonian War, but it was subsequently taken by the Russian Empire in the 1710 Capitulation of Estonia and Livonia and the 1721 Treaty of Nystad, following the Great Northern War. It belonged to Imperial Russian Governorate of Livonia then.
The town became part of independent Estonia in 1918 following World War I.
During the Great Northern War, the University of Dorpat (Tartu) was relocated to Pernau from 1699-1710. The university has a branch campus in Pärnu today (1,000 students in the 2004/2005 school year)
