Star Trek: 10 Things You Never Knew About Chakotay
5. Lieutenant Commander Chakotay
During all of Star Trek: Voyager's seven season run, Chakotay wore the rank insignia of a Lieutenant Commander, not a full commander. This was shown on his collar, with two gold bars and one black one. He, along with the rest of the Maquis crew, wore the insignia of a provisional officer.
Though he was always referred to as a full commander, he was in fact only a lieutenant commander when he resigned his commission. This was also the rank of Cavitt, the original executive officer of Voyager, who was killed by the Caretaker's displacement wave. While it has become something of a tradition that the XO of a starship is a full commander, that wasn't always the case. Raffi would become another example of this.
Chakotay, having already served as an officer, would have been entitled to wear standard rank insignia, much like Tom Paris elected to. In solidarity with the rest of his crew, he chose to wear this reminder that, while he was committed to both crews integrating and working together, he would always be in a position to represent them while wearing a Starfleet uniform.