The Marine Uniform Regulations of 1859 do not seem to authorize any special trousers for the Commandant.
From the 1859 regulation:
The uniform trowsers for both offices, and enlisted men, shall, in cold weather, be made of cloth, with French pockets, made loose, and to spread well over the boot, of white and light blue mixed, commonly called sky blue mixture.
Officers not serving in line with troops, may wear dark blue cloth trowsers, with a welt of scarlet cloth, let into each outer seam.
In warm weather the uniform trowsers for both officers and enlisted men, shall be of white linen. Both the cloth and linen trowsers shall be cut for enlisted men as shown in plates.
The cloth for the trowsers of enlisted men shall be of kesey.
Cloth trowsers for Commissioned Officers shall have a welt of scarlet, three-sixteenths of an inch in diameter, let into the outer seam
For Sergeant major, Quartermaster Sergeant, Drum Major, Chief Musicians, and Musicians, a scarlet cord three-sixteenths of an inch in diameter, down the outer seam
Note that the regulation do not specify the style of trousers worn by officers and the exact style was left up to the officer. During the Civil War officer trousers usually came in three styles, strait leg, close fitting, and Peg tops. Most photographs I have seen show officers wearing strait leg trousers of either dark blue, sky blue, or white. I do not recall seeing photographs of officers wearing Peg tops or close trousers.