Capt Lee Joon-seok and the other homicide defendants a first mate, a second mate and the chief engineer could face the death penalty if convicted, according to the Supreme Court, though no one has been executed in South Korea since 1997.
The 11 others were indicted for alleged negligence and abandoning passengers in need when the ship sank on April 16, according to prosecutors.
The indicted crew members were among the first group of people rescued when the Sewol began badly listing, and all were arrested last month.
Lee initially told passengers to stay in their cabins and took about half an hour to issue an evacuation order but it's not known if his message was ever conveyed to passengers. In a video taken by the coast guard, he was seen escaping the ferry in his underwear to a rescue boat while many passengers were still in the sinking ship.
The head of the ferry's owner, Chonghaejin Marine Co Ltd, and four other company employees have also been arrested. Authorities suspect improper stowage and overloading of cargo may have contributed to the disaster.
About one month after the sinking, 284 bodies have been retrieved and 20 others are listed as missing. Only 172 people, including 22 of the ship's 29 crew members, survived. Most of the victims were students from a single high school near Seoul who were travelling to the southern tourist island of Jeju.