A rowing shoe system for use by a rower in a racing boat has a footboard adapted to be secured in a boat, a pair of shoe liners and a pair of shoe shells. The pair of shoe liners are sized to receive the feet of a rower, are made out of anti-microbial material, and have a flexible exterior surface and a flexible interior surface configured to fit over substantially the entire foot of the rower. The pair of shoe shells are detachably securable to the footboard in a rowing position and have an interior sized to receive the flexible shoe liners. The shoe shells have openings therein to ventilate the rower's feet, and the shoe liners are removable from the shoe shells. The rowing shoe system may include a plurality of pairs of shoe liners of different foot sizes.