Abdimalik Jones, who said he is from San Diego, was arrested yesterday in southern Somalia, said African Union spokesman Col Paul Njuguna.
The American was arrested in the southern port of Barawe, 10 miles (180 kilometers) southwest of Mogadishu, said Njuguna.
Jones claimed he fled al-Shabab because of rifts within the rebel group, said an official with Somali security forces who insisted on anonymity because he is not authorised to speak to the press. Jones is missing the index finger of his right hand, said the official.
In September 2013, al-Shabab fighters killed Omar Hammami, a rapping American jihadi from Alabama who was on the FBI's Most Wanted list with a USD 5 million reward for his capture. He was killed in an ambush ordered by al-Shabab's leader Ahmed Abdi Godane, who was later killed in a US airstrike last year.
Despite losing key strongholds in Somalia, al-Shabab is fighting the Somali government and African Union forces and continues to carry out deadly bombing attacks across Somalia and neighbouring countries.