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According to Oregon Geographic Names, the county is named for the town of Union. Union County was originally part of Baker County (which was originally a part of Wasco County, which was originally part of Clackamas County). The northern end of the Grande Ronde Valley was the first part to be settled. During the 1860s, population growth in eastern Oregon prompted the State Legislature to split Umatilla and Baker Counties from Wasco County in 1862. Further settlement in the Grande Ronde Valley led to the division of Baker County to create Union County on October 14, 1864. The county doubled in population between 1880 and 1890.
The choice of a county seat resulted in competition, based on geography and on economic and population growth, between La Grande and the city of Union. The county seat alternated between Union and La Grande until it permanently came to rest at La Grande in 1905. Between 1875 and 1913, adjustments were made between Union County's borders and the borders of Baker, Umatilla, and Wallowa counties.