Question

Who was the southerner that commanded union ships during the capture of the Mississippi River ?

Answer 1

The southerner that commanded Union ships during the capture of the Mississippi River was David Farragut.

In December of 1861 Farragut was assigned to command the blockade squadron of the Union to the west of the Gulf of Mexico; with orders to enter the Mississippi River and capture New Orleans, a port through which the Confederacy received much of its war supplies.

Although the Department of War had recommended that he should first reduce the two forts that protected the access to the river, Farragut successfully carried out his own plan to pass between the enemy batteries taking advantage of the darkness on April 24, 1862, with his ship "Hartford". His naval force, once it had penetrated, destroyed most of the Confederate squadron that was anchored behind the forts. The troops of the Union could then disembark under the protection of Farragut's ships, thus achieving the surrender of New Orleans.

Answer 2

I think it's Ulysses S Grant.
Hope this helps somewhat. 
Let me know if this incorrect for others know. 
And even if it is right let me know.