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.
Historian have identified the schooner to be the last ship known to bring African captives to the US, Reuters reports.
The vessel 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 Sylviane Diouf, a noted historian of the African diaspora.
The ship is believed to have been intentionally sunk in 1860 to hide evidence of its use in the slave trade, according to National Geographic.
The team behind the search for the Clotilda discovered a ship with its identifying features under water in a section of the Mobile River, according to National Geographic, unveiling "a 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 Clotilda’s dimensions and its other unique characteristics, such as planks of southern yellow pine over white oak frames.