The previous commander of the CSS Arkansas, William McBlair? and John Guthrie were detached from the Arkansas and ordered to the east.
Following his removal from the CSS Arkansas project at Yazoo City (Greenwood, Ms.) Guthrie served at the Richmond and Wilmington naval stations.
On February 4, 1863, he was posted to Chattahoochee, Florida, and commanded the CSS Chattahoochee. Following the boiler explosion aboard on May 27, 1863, he commanded the initial voyage of the North Carolina state-owned blockade runner A.D. Vance (also known as the Advance) in February 1864.
Guthrie was then sent to superintend the Halifax, North Carolina, Navy Yard, where he assisted with the material requirements of then famed ironclad CSS Albemarle.
After the loss of the Albemarle to William Cushing's famed "torpedo," he returned to blockade running. On March 23, 1865, he was appointed military aide to North Carolina governor Zebulon B. Vance.