Isondiga operated in waters around Savannah, Georgia, and in Saint Augustine Creek, Florida, from April 1863 to December 1864, Lieutenant Joel S. Kennard commanding. She accompanied ironclad ram CSS Atlanta in the engagement in which Atlanta was captured on June 17, 1863.
She escaped from Savannah on December 21, 1864 before the city fell to the forces of U.S. General William T. Sherman. She was later burned by her commanding officer and crew to prevent seizure by the Union.
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