In April 1862, Finegan assumed command of Middle and East Florida from Brigadier General
James H. Trapier. Soon thereafter, he suffered some embarrassment surrounding the wreck of the
blockade runner Kate at Mosquito Inlet (the modern
Ponce de Leon Inlet). Her cargo of rifles, ammunition, medical supplies, blankets, and shoes was plundered by civilians. Attempts to recover these items took months before he issued a public appeal. Eventually, most of the rifles were found, but the other supplies were never recovered. Also in 1862, recognizing the importance of Florida beef to the Confederate cause, Finegan gave cattle baron
Jacob Summerlin permission to select thirty men from the state troops under his command to assist in rounding up herds to drive north. At this time, the principal Confederate military post in east Florida was dubbed "Camp Finegan" to honor the state's highest-ranking officer. It was about west of
Jacksonville, south of the rail line near modern
Marietta. In 1863, Finegan complained of the large quantity of
rum making its way from the
West Indies into Florida. Smugglers were buying it in
Cuba for a mere seventeen cents per gallon, only to sell it in the blockaded state for twenty-five dollars per gallon. He urged Governor
John Milton to confiscate the "vile article" and destroy it before it could impact army and civilian morals. In February 1864, General
P.G.T. Beauregard began rushing reinforcements to Finegan after Confederate officials became aware of a build-up of Federal troops in the occupied city of Jacksonville. As Florida was a vital supply route and source of beef to the other southern states, they could not allow it to fall completely into Union hands. On February 20, 1864, Finegan stopped a Federal advance from Jacksonville under General
Truman Seymour that was intent upon capturing the state capitol at
Tallahassee. Their two armies clashed at the
Battle of Olustee, where Finegan's men defeated the
Union Army and forced them to flee back beyond the
Saint Johns River. Critics have faulted Finegan for failing to exploit his victory by pursuing his retreating enemy, contenting himself by salvaging their arms and ammunition from the battlefield. But, his victory was one rare bright spot in an otherwise gloomy year for the dying Confederacy. Some Finegan detractors believe he did little more to contribute to the Confederate victory at Olustee than to shuttle troops forward to General
Alfred H. Colquitt of
Georgia, whom they credit for thwarting the Federal advance. They point out that Finegan was quickly relieved of his command over the state troops, replaced by Major General
James Patton Anderson. But this change in command was necessary as Finegan was ordered to lead the
Florida Brigade in the
Army of Northern Virginia, where he served effectively until near the end of the war. .Col
David Lang was the brigade's last commander before the surrender after the
Battle of Appomattox Court House. ==Postbellum career==