We analyzed a 16-year (1996-2011) time series of catch and effort data for 23 species with mean weights ranging from 0.8 kg to 224 kg, recorded by observers in the Hawaii-based deep-set longline fishery. Over this time period, domestic fishing effort, as numbers of hooks set in the core Hawaii-based fishing ground, has increased fourfold. The standardized aggregated annual catch rate for 9 small (<15 kg) species increased about 25% while for 14 large species (>15 kg) it decreased about 50% over the 16-year period. A size-based ecosystem model for the subtropical Pacific captures this pattern well as a response to increased fishing effort. Further, the model projects a decline in the abundance of fishes larger than 15 kg results in an increase in abundance of animals from 0.1 to 15 kg but with minimal subsequent cascade to sizes smaller than 0.1 kg. These results suggest that size-based predation plays a key role in structuring the subtropical ecosystem. These changes in ecosystem size structure show up in the fishery in various ways. The non-commercial species lancetfish (mean weight 7 kg) has now surpassed the target species, bigeye tuna, as the species with the highest annual catch rate. Based on the increase in snake mackerel (mean weight 0.8 kg) and lancetfish catches, the discards in the fishery are estimated to have increased from 30 to 40% of the total catch.