To answer questions from the WCPFC Scientific Committee (SC12) , SEAPODYM model was used to investigate skipjack spatial structure, connectivity and impact of equatorial purse seine fishing on distant fisheries as the Japanese domestic fisheries. A new reference solution of SEAPODYM to skipjack achieved at coarse resolution showed improved fit to data and realistic parameterization of biological parameters, and was downscaled to a higher resolution oceanic forcing. Simulations with different fishing scenarios indicate weak to moderate connectivity between equatorial purse seine fishing ground and the Japanese domestic waters, while environmental variability associated to El Nino is predicted to impact the recruitment. After a tendency to decrease over 2006-12, the larvae recruitment in North west Pacific shows an opposite increasing trend in the recent years in concordance with favorable conditions associated to 2014-15 El Niño event. Adult stock is expected to increase in 2016-17.