However, before "Tioga" could become an effective part of the Potomac Flotilla, a change of orders reassigned her to the newly established West India Squadron, formed – under the command of Commodore Charles Wilkes – to counter the threat posed by the recent commissioning of the Confederate commerce raider "Florida" and the expected activation of the steam warship then being built for the South in England under the designation 290 which would prey on Northern shipping as "Alabama". While "Tioga" never encountered either of these adversaries which would win renown under Confederate colors, she did compile an impressive score against blockade runners.