A rod and reel storage system for a fishing boat. In one embodiment, trays are mounted in the gunwale walls and provided with guide tubes through which stored fishing rods extend into the gunwale cavity. The trays have separate compartments which receive and hold the reels. Hinged hatches on the gunwales cover gunwale hatchways that provide access to stored rods and reels. In another embodiment, a reel storage compartment is located to one side of the control console of the boat, and tubes extend forwardly beneath the bow fishing deck to hold the rods. A hinged door opens and closes the storage compartment and may be locked closed.