The Pacific Island countries have a substantial socio-economic dependency on fisheries. Skipjack tuna is one of the most important species in the Western Central Pacific (WCP) and its catches in this region exhibit a spatio-temporal variability influenced by ocean conditions, mainly the El Niño-Southern Oscillation (ENSO). This study investigates the relationship between skipjack tuna catch amounts and environmental variables in the equatorial Pacific during 1990-2014, and evaluates the potential predictability of the catches based on their statistical relationship. A series of regressed and reconstructed spatial patterns of upper-ocean temperature, salinity, currents and precipitation represent ENSO-like variability, and their principal component time series are used to estimate the predictability of skipjack tuna catches in the Federated States of Micronesia (FSM). ENSO-like variability depicted from 100 m temperature and 5 m salinity in the equatorial Pacific exhibit a significant predictability for the annual catch amount in the FSM for several years with a training period of > 20 years. This suggests that the subsurface temperature or near surface salinity can be a better predictor of ecosystem variability than widely used sea surface temperature. Applications of this result to other species could have broad implications for the fishery industry in the WCP.