The Mindanao Current (MC) bridges the North Pacific low-latitude western boundary current system region and the Indonesian Seas by supplying the North Pacific waters to the Indonesian Throughflow. Although the previous study speculated that the diapycnal mixing along the MC might be strong on the basis of the water mass analysis of the gridded climatologic dataset, the real spatial distribution of diapycnal mixing along the MC has remained to be clarified. We tackle this question here by applying a finescale parameterization to temperature and salinity profiles obtained using two rapid-sampling profiling Argo floats that drifted along the MC. The western boundary (WB) region close to the Mindanao Islands and the Sangihe Strait are the two mixing hotspots along the MC, with energy dissipation rate ε and diapycnal diffusivity Kρ enhanced up to?~?10–6 W kg?1 and?~?10–3 m2 s?1, respectively. Except for the above two mixing hotspots, the turbulent mixing along the MC is mostly weak, with ε and Kρ to be 10–11–10–9 W kg?1 and 10–6–10–5 m2 s?1, respectively. Strong mixing in the Sangihe Strait can be basically attributed to the existence of internal tides, whereas strong mixing in the WB region suggests the existence of internal lee waves. We also find that water mass transformation along the MC mainly occurs in the Sangihe Strait where the water masses are subjected to strong turbulent mixing during a long residence time.