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On December 28, 1847, the Provisional Legislature created Linn County from the southern portion of Champoeg (later Marion) County. The boundaries were altered in 1851 and 1854 with the creation of Lane and Wasco Counties. The county seat was originally located in Calapooia (later known as Brownsville), but in 1851 the Territorial Legislature passed an act establishing Albany as the county seat. A special election in 1856 reaffirmed Albany as the county seat.
The county is named for Missouri Senator Lewis F. Linn.