Ataloa Lodge Museum: Housed on the Bacone College Campus at 2299 Old Bacone Rd., This museum contains a vast privately-owned collection of Native American art.
Five Civilized Tribes Museum: Exhibits on the art, history and culture of the Five Civilized Tribes housed at the historic Union Indian Agency Building at the top of Honor Heights Park.
Three Rivers Museum: Muskogee was founded near the intersection of the Arkansas, Grand and Verdigris Rivers. The Three Rivers Museum chronicles the story of Muskogee and the Three Rivers area.
USS Batfish War Memorial Park Museum: The USS Batfish sank three enemy subs and eleven other vessels during her commission. Located at the Port of Muskogee, visitors can tour the submarine and war park.