An estimation method based on sliding discrete Fourier transform (SDFT) integrated with phase-locked loop is introduced for vibration mode estimation of single-link flexible manipulator (SLFM). Based on Euler-Lagrangian state space model and first vibration mode frequency, SDFT PLL is designed to estimate first vibration mode and harmonics that appear in tip deflection. Instantaneous change in tip deflection due to payload conditions is tracked by adaptive sampling frequency control. State-space model, estimated amplitudes and frequencies of tip deflection including harmonics are validated through experiments. Furthermore, experimental investigation on SLFM demonstrates the effectiveness of online vibration mode estimation method in presence of noise and offset. Index Terms-Phase-locked loop (PLL), single-link flexible manipulator (SLFM), sliding discrete Fourier transform, vibration mode estimation.