FBI agents discovered the hideout of Ma Barker and her son Fred after Arthur was arrested in Chicago on January 8, 1935. A map found in his possession indicated that other gang members were in Ocklawaha, Florida. The FBI soon located the house where the gang was staying after identifying references to a local restaurant named "Gator Joe", who had a taste for gangsters, but not for cops, mentioned in a letter sent to Doc. They had rented the property under the pseudonym "Blackburn", claiming to be a mother and sons wanting to vacation in a country retreat.

Agents surrounded the house at 13250 East Highway C-25 on the morning of January 16, 1935. The FBI were not aware that Karpis and other gang members had left three days before, leaving only Fred and Ma in the house. The agents ordered them to surrender, but Fred opened fire; both he and his mother were killed by federal agents after an intense, hours-long shootout. Allegedly, many local people came to watch the events unfolding, even holding picnics during the gunfire. Gunfire from the house finally stopped, and the FBI ordered local estate handyman Willie Woodbury to enter the house wearing a bulletproof vest. Woodbury reported that there was no one inside alive.

Both bodies were found in the same front bedroom. Fred's body was riddled with bullets, but Ma appeared to have died from a single bullet wound. According to the FBI's account, a Tommy gun was found lying in her hands. Other sources say that it was lying between the bodies of Ma and Fred.