Shipmaster

Ship Master is a Covenant title, only given to Elites before the Civil War. As described by their title, Ship Masters often command a single Covenant starship. The size of the starship does not seem to matter, whether a Covenant Frigate or a Reverence-class Cruiser. The title usually goes to an Elite, Brute, or Minor Prophet. Ship Masters usually have bodyguards, such as a Hunter pair.

Rank
A Ship Master is a Covenant title for a high ranking Covenant Elite who is in command of a single starship. As per to denote their high ranking status, most Ship Masters usually have bodyguards, such as a Hunter pair or a Lance. While Ship Masters hold their individual power to command, they still fall under the chain of command, taking orders from their fleet's Supreme Commander or Imperial Admiral.

From what the UNSC has observed, the Ship Master of a particular ship commands from the command center of their vessel, the rough equivalent of a UNSC starship's bridge. There they oversee and supervise the running of the ship, and give orders during battle. They command the ship from a platform raised off the deck, surrounded by holoscreens displaying relevant information.

Before Halo: Ghosts of Onyx, it was assumed that only Zealots could hold the rank of Ship Master. However, after killing the previous Ship Master of their vessel, the Incorruptible, Major Domo Voro 'Mantakree was given the title of Ship Master, and then promoted to Zealot so that he could become a Fleet Master, in charge of a task force sent to Onyx. Given the sheer size of the Covenant, the majority of Ship Masters are probably either Major Domos or Ultras.

As such, higher ranks than Zealot may hold command positions over a starship. The Arbiter, should their role call for it, could be given command of a ship. Councilors could also have the potential to be a ship master, having even Zealots subordinate to them. These ranks could theoretically be considered the Ship Master of a particular ship; most likely the flagship of the fleet. There are also Brute equivalents to the Ship Master, called Alpha Jiralhanae - these may be equivalent to the entire Zealot range.

Physical Appearance
Elite Ship Masters featured thus far don't appear to have any changes to their armor to distinguish themselves from other members of their rank (it is impossible to tell a Zealot Ship Master apart from a Zealot Field Master based on their armor, for example). Other types of Ship Masters, such as Alpha Brutes or Minor Prophets, are yet to be sighted. It is unknown if their armor would be different to denote their rank.

Halo: Combat Evolved
Only one Ship Master is seen, the Ship Master of the Truth and Reconciliation. He was killed by the Master Chief during his infiltration of the ship to find and rescue Captain Keyes. As a senior officer, his combat skills are honed, and he makes far fewer tactical mistakes than, for example, Minor Domo or Major Domo.

Halo: Ghosts of Onyx
Two Ship Masters are mentioned in Ghosts of Onyx. The first is Tano 'Inanraree, and the second is his successor and killer, Voro 'Mantakree. 'Mantakree later was given the office of Fleet Master to pursue the Incorruptible.

Halo 3
In Halo 3, Rtas 'Vadum holds the rank of Ship Master. He commands the ships that glass the city of Voi.

Trivia

 * Though speculated to be the Covenant equivalents to UNSC Navy Captains, they may wield more influence than expected - Ship Masters have been seen in Halo: The Flood and Halo 3 directing relatively small battlegroups, instead of single ships.
 * So far, the only elite ranks confirmed holding the title of ship master are Zealots, Ultras and Major Domos.

Known Ship Masters

 * Orna 'Fulsamee, alleged Ship Master of the Truth and Reconciliation
 * Tano 'Inanraree, former Ship Master of the Incorruptible
 * Voro 'Mantakree, Ship Master of the Incorruptible
 * 'Qunu, Ship Master of the Far Sight Lost
 * Rtas 'Vadum, Ship Master of the Shadow of Intent