Optical flow sensing techniques are promising for obstacle avoidance, distance regulation, and moving target tracking, particularly for small mobile robots with limited power and payload constraints. Most optical flow sensing experimental work has been done on mobile platforms which are relatively steady in rotation, unlike the pitching motion expected on flapping wing flyers. In order to assess the feasibility of using optical flow to control an indoor flapping flyer, a 7 gram commercially available ornithopter airframe was equipped with on-board camera and CPU module with mass of 2.5 grams and 2.6 gram battery. An experiment was conducted capturing optical flow information during flapping and gliding flight on the same platform. As expected, flapping introduced substantial systematic bias to the direction estimates to the point of flipping the true direction periodically. Nonetheless, since the optical flow results oscillated at the same frequency as the flapping wings, one could disambiguate the jittering optical flow measurements by correlating these with real-time feedback from the motor current or voltage. Motor Back-EMF was introduced as a filtering signal after corroborating its correlation with the wingstroke position. A reconstructed wingstroke signal was then used to disambiguate the motion estimated in an experiment that constrained the robot to flap down a string. It is envisioned that this technique can be implemented on-board the flapping flyer due to its low computational complexity.