This paper describes the design and implementation of a Cotton flow monitoring and control system for cotton gins. The system comprises of new flow sensors utilizing electro-optic technology. They combine emitters and detectors mounted on the air pipe of the gin, pass the module feeder. As the cotton passes through, it is illuminated by the emitters. The detectors which are positioned across the chute detect the light pulses. The pulse count is relative to the volume and density of the cotton. They are used to estimate the mass of the cotton passing through the air pipe. These continuous measurements are transmitted to a control unit which calculates a correction signal for the feed motors of the module feeder. This system, in a closed loop operation is capable of compensating, for variation in feed conditions. The speed of the module feeder is adjusted is compensated for module highs, density, gaps between modules and even overcome clogging due to module collapse and feed of slugs.