Donald P. Hayes gave no reason for Guy D. Johnson's resignation, which took effect on Friday.
But it comes just days after the company announced it will trim service to some communities, require seniors to pay higher fares and consider introducing slot machines on some vessels to raise revenue.
In a three-line news release, Hayes simply acknowledges Johnson's service and contribution to the board.
The ferry service appointed Johnson to its board of directors in August 2012.
At the time, it said he was a partner in Victoria, B.C.'s Brentwood Bay Lodge and Spa, held a master's degree in business administration from the University of Illinois, and was a senior executive of Sirius Satellite Radio and Thomson Multimedia.