The North Pacific subtropical gyre (NPSG) plays a major part in the export of carbon and other nutrients to the deep ocean(1). Primary production in the NPSG has increased in recent decades despite a reduction in nutrient supply to surface waters(2,3). It is thought that this apparent paradox can be explained by a shift in plankton community structure from mostly eukaryotes to mostly nitrogen-fixing prokaryotes(2-4). It remains uncertain, however, whether the plankton community domain shift can be linked to cyclical climate variability or a long-term global warming trend(5). Here we analyse records of bulk and amino-acid-specific N-15/N-14 isotopic ratios (delta N-15) preserved in the skeletons of long-lived deep-sea proteinaceous corals collected from the Hawaiian archipelago; these isotopic records serve as a proxy for the source of nitrogen-supported export production through time. We find that the recent increase in nitrogen fixation is the continuation of a much larger, centennial-scale trend. After a millennium of relatively minor fluctuation, delta N-15 decreases between 1850 and the present. The total shift in delta N-15 of -2 per mil over this period is comparable to the total change in global mean sedimentary delta N-15 across the Pleistocene-Holocene transition, but it is happening an order of magnitude faster(6). We use a steady-state model and find that the isotopic mass balance between nitrate and nitrogen fixation implies a 17 to 27 per cent increase in nitrogen fixation over this time period. A comparison with independent records(7,8) suggests that the increase in nitrogen fixation might be linked to Northern Hemisphere climate change since the end of the Little Ice Age.