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Prior to the 1840's, Alpena was inhabited by the local Indians of the Area. As the white man moved in the Indians were quickly displaced. Like most northern Michigan cities located on or near the waters of the Great Lakes, the Alpena area was rich with trees and the Thunder Bay River made the harvesting of the trees highly profitable.

The port of Alpena was originally laid out in 1840 and was named "Animickee" for the Chippewa's Chief who signed the treaty of 1826, which was negotiated by Henry R. Schoolcraft. The word "Animickee" means thunder.

In 1848 the area was renamed Fremont by the city founders after a presidential candidate. The name Fremont stuck until 1858, when it was changed back to Alpena. The city of Alpena was founded in 1871, at that time it had approximately 3500 residents.

In 1887 the Detroit and Mackinaw Railroad reached Alpena. The rails helped lay the foundation of the diversified industries it has today.

The Fletcher Pulp Mill was built in 1886 and the Paper Mill in 1898.