 Greene later served on , and from 1854 to 1856 was stationed at the Boston Navy Yard.Promoted to commander on September 14, 1855, he served as lighthouse inspector, First District, from November 1857, until 1860, when he assumed command of the Mare Island Naval Shipyard, near San Francisco, California.He was promoted to captain on July 16, 1862, and commanded , and later , in the East Gulf Squadron.