We study the relationship between changes in the equatorial stratification and low frequency ENSO modulation in a coupled general circulation model (CGCM). The stratification is intensified at upper levels in the western and central equatorial Pacific ocean during periods of high ENSO amplitude. Furthermore, changes in the stratification are connected with a westward-equatorward propagation of subsurface temperature anomalies originating in the central-south tropical Pacific. The analysis of the wind stress projection coefficient onto the oceanic baroclinic modes suggests that the contribution of the higher modes increases in the western and central equatorial Pacific during periods of high ENSO amplitude. This result supports the hypothesis of oceanic tunnels from the South tropical Pacific to explain the low frequency ENSO modulation.1