The oceanographic consequences of climate change are increasingly well documented, but the biological impacts of this change on marine species much less so, in large part because of few long-term data sets. Using otolith analysis, we reconstructed historical changes in annual growth rates for the juveniles of eight long-lived fish species in the southwest Pacific, from as early as 1861. Six of the eight species show significant changes in growth rates during the last century, with the pattern differing systematically with depth. Increasing temperatures near the ocean surface correlate with increasing growth rates by species found in depths <250 m, whereas growth rates of deep-water (>1,000 m) species have declined substantially during the last century, which correlates with evidence of long-term cooling at these depths. The observations suggest that global climate change has enhanced some elements of productivity of the shallow-water stocks but also has reduced the productivity, and possibly the resilience, of the already slow-growing deep-water species.