The tropical instability waves (TIWs) in the eastern tropical Pacific have generally been considered as surface-intensified structures resembling the first baroclinic mode. Here, we report on the existence of subsurface-intensified TIWs on the equator. These TIWs are primarily manifested in zonal velocities, inducing maximum velocity oscillations at 70–90 m depth with amplitudes of 0.1–0.2 m/s and periods of 5–20 days. They account for ~20% of the variance at 5- to 30-day periods, with another ~50% being contributed by the surface-intensified TIWs. These waves are most significant during the TIW seasons; they are energized in part by barotropic instabilities and usually last for 3–7 months. Via interacting with the mean flow, they can induce strong out-of-phase shear changes between ~50-m depth and just above the Equatorial Undercurrent core and may lead to complex diapycnal mixing structures. Their horizontal structures, generation mechanism(s), and large-scale impacts remain to be disclosed.