Spider mites have become a severe leaf feeding pest on cotton during the last few years. Their feeding on leaves disturb some important physiological processes, consequently decreasing the productivity of the plants. Studies are lacking on the physiological and ultrastructural changes caused by mite injury. Therefore, a study was conducted to understand mite injury at the physiological and cellular level. Mite injury interfered with the function of the stomatal apparatus causing stomatal closure. This drastically reduced photosynthesis, chlorophyll content, stomatal conductance, and transpiration rate. Cytological studies using light and electron microscopy showed that the spongy mesophyll cells were damaged and became necrotic and sometimes, in severe cases, the palisade cells were also damaged, causing the chloroplasts to move out of the cells through damaged membranes.