This paper presents a robust position tracking controller for motor-driven flexible joint manipulators using only the motor angle measurement. The control problem is not easy because the link position is hard to estimate in the presence of parameter uncertainties. The proposed controller consists of a feedback linearization controller (FLC) and two proportional-integral observers (PIOs) that estimate both system states including the link position and an equivalent disturbance for compensating the parameter uncertainties. Comparative computer simulations are conducted to demonstrate the effectiveness of the proposed control algorithm.