When the American Civil War broke out in 1861, he was the highest-ranking and longest-serving USN officer to join the Confederate side.

He was born in New Orleans when it was a Spanish colonial possession, one of 12 children of Pierre George Rousseau and Marie Catherine Milhet.

With the assistance of David Porter, the commandant of New Orleans, Rousseau was appointed a midshipman on January 16, 1809, the start of a naval career of 56 years.

[3] On November 1, he was given command of Thompson's Island naval station, near present-day Key West, where he conducted several anti-pirate operations.

[2] On August 1, 1838, he was ordered to survey the coast of the Gulf of Mexico for locations for lighthouses; his report and recommendations were presented by 1842.

[2] When the South seceded from the Union, he resigned from the USN on January 31, 1861,[2] effective February 11,[1] and joined the CSN.

Rousseau traveled to Montgomery, Alabama, to engage in the discussion of Confederate naval defences.

[2] He purchased the merchant steamer Habana, which was converted into the Confederacy's first steam cruiser, CSS Sumter.

[2] (Sumter, under the command of Raphael Semmes, embarked on commerce raiding and captured 18 prizes in its six-month career.)

[2] On May 4[1] or 10,[2] 1865, he surrendered with other Confederate officers and men at Nanna Hubba Bluff, Alabama, and gave his parole not to take up arms against the United States.