Abstract We report the observation of various harmonic mode-locking (HML) of a dual-wavelength all-fiber laser mode-locked with different repetition rates, and show the stability of the repetition rate difference. Interestingly, a state of second-order HML at both wavelengths is achieved. The repetition rate difference is recorded, resulting in a standard deviation of 9.3 Hz, though the repetition rates of both wavelengths fluctuate ∼ 860 Hz. It enriches the nonlinear dynamics of mode-locked lasers, and has potential applications related to the dual-comb based on free-running lasers, provided that the stability of HML is further improved.