On September 11, 1998, about 2315 Alaska daylight time, a Beech 1900C airplane, N1563C, sustained substantial damage during landing at the St. Mary's Airport, St. Mary's, Alaska. The airplane was being operated as Flight 91 on an instrument flight rules (IFR) cargo flight under Title 14 CFR Part 135 when the accident occurred. The airplane was operated by Alaska Central Express Inc., Anchorage, Alaska. The certificated airline transport pilot, the sole occupant, was not injured. Visual meteorological conditions prevailed at the destination. An IFR flight plan was filed. The flight originated at the Anchorage International Airport, Anchorage, at 2133. The Director of Operations for the operator reported the pilot was making a visual approach during dark night conditions to runway 16 at St. Mary's. On the downwind portion of the landing approach, the pilot selected flaps down, but nothing happened. The pilot's trouble shooting did not remedy the flap problem, and he elected to make a flaps-up landing. The airplane settled onto the runway with the landing gear retracted. The airplane received damage to the underside, aft end of the fuselage, the engine nacelles, and propellers. The airplane is equipped with a landing gear warning horn, and a red cautionary annunciator light in the landing gear handle. In the pilot/operator report (NTSB form 6120.1/2) submitted by the operator, the operator indicated there was no mechanical malfunction with the airplane.