The Alabama Historical Commission, in a post on its Facebook page, called the effort to locate the ship, the Clotilda, a year-long scientific investigation..
The Clotilda was discovered by a company called SEARCH Inc in collaboration with the commission and the Smithsonian National Museum of African American History and Culture.
Historians have documented the Clotilda as the last ship known to bring African captives to the US. It operated in secret, decades after Congress banned the importation of slaves into the country in 1807.
The Clotilda carried 110 men, women and children from Africa to Alabama in 1860, according to the 2007 book Dreams of Africa in Alabama by Sylviane Anna Diouf, who relied on testimony from the slave traders and their captives.
The ship is believed to have been intentionally sunk in 1860 to hide evidence of its use in the slave trade.
Three years later, in the middle of the civil war, President Abraham Lincoln signed the Emancipation Proclamation declaring the end of slavery in the US.
The discovery of the Clotilda sheds new light on a lost chapter of American history, said Fredrik Hiebert, archaeologist-in-residence at the National Geographic Society, which supported the search.
Researchers used insurance records to determine the Clotildas dimensions and its other unique characteristics, such as planks of southern yellow pine over white oak frames, according to National Geographic.
The team behind the search for the Clotilda discovered a ship with its identifying features underwater in a section of the Mobile River, according to National Geographic.
A representative from the Alabama Historical Commission could not be reached for comment late on Wednesday.