Cut crab and Mitsuba into large pieces. Separate Shimeji mushrooms into individual pieces.
Crack eggs into a container and beat until smooth. Add miso and water and combine with the beaten eggs.
Divide crab, Mitsuba and mushrooms evenly into two heat-proof cups. Evenly distribute the egg-miso-water mixture over the ingredients. Cover cups with plastic wrap leaving a small opening for steam to escape. Microwave at 1200W for 1 minute 40 seconds (cooking time depends on the wattage of your microwave) or until egg mixture is heated through and set.
Allow the cups to sit in the microwave without power for an additional 5 minutes for steaming.