In August 1862, Molineux assisted in raising the
159th New York Infantry Regiment. He was initially assigned as lieutenant colonel and second in command; when the unit's first commander,
Homer Augustus Nelson, resigned, Molineux was promoted to
colonel and assigned as regimental commander. The 159th New York served under
Nathaniel P. Banks, commander of the
Department of the Gulf, and Molineux took part in battles including the
Siege of Port Hudson,
Red River campaign, and
Battle of Irish Bend. He also acted as commander of 2nd Brigade, 2nd Division,
XIX Corps, and was wounded in the jaw at Irish Bend in April 1863. While convalescing, he took part in the Union response to the
New York City draft riots. After recovering from his wounds, he returned to duty as assistant
inspector general of the Department of the Mississippi. He subsequently served as the department's
provost marshal and commissioner for prisoner exchanges. Molineux was next appointed to command Louisiana's
Lafourche Military District, where his duties included organizing pro-Union state troops and guarding the construction site during the building of
Bailey's Dam near
Alexandria, Louisiana in April and May 1864. He was later ordered to Virginia, where he took part in the
Siege of Petersburg and organized a provisional division of the XIX Corps. Molineux took part in the
Valley campaigns of 1864, and he earned
brevet promotion to
brigadier general for his superior performance of duty at the September 1864
Battle of Fisher's Hill and
Third Battle of Winchester, and the October 1864
Battle of Cedar Creek. He was then assigned to
Georgia, where he participated in
Sherman's March to the Sea during November and December 1864. In early 1865, he was assigned to command the Military District of Northern
Georgia, including the coastal defenses of
Savannah,
Fort Pulaski and
Tybee Island. While in this position, Molineux directed the March 1865 rescue of S.S.
Lawrence, a cargo ship that had become grounded. Military members and civilian volunteers succeeded at saving the ship and its cargo of cotton, and New York City
underwriters presented Molineux with a
silver service as a token of their appreciation. Molineux also seized Confederate stores and infrastructure in Savannah, including gold bullion and cotton worth over $10 million ($210 million in 2025), as well as factories, warehouses, and government buildings, all of which he turned over to the U.S. government for final disposition. Molineux received brevet promotion to major general in recognition of his accomplishments while serving in Georgia. ==Later career==