Marine ecosystems of the Southern Ocean are particularly vulnerable to ocean acidification. Antarctic krill (Euphausia superba; hereafter krill) is the key pelagic species of the region and its largest fishery resource. There is therefore concern about the combined effects of climate change, ocean acidification and an expanding fishery on krill and ultimately, their dependent predators--whales, seals and penguins. However, little is known about the sensitivity of krill to ocean acidification. Juvenile and adult krill are already exposed to variable seawater carbonate chemistry because they occupy a range of habitats and migrate both vertically and horizontally on a daily and seasonal basis. Moreover, krill eggs sink from the surface to hatch at 700-1,000m (ref. ), where the carbon dioxide partial pressure (pCO2) in sea water is already greater than it is in the atmosphere. Krill eggs sink passively and so cannot avoid these conditions. Here we describe the sensitivity of krill egg hatch rates to increased CO2, and present a circumpolar risk map of krill hatching success under projected pCO2 levels. We find that important krill habitats of the Weddell Sea and the Haakon VII Sea to the east are likely to become high-risk areas for krill recruitment within a century. Furthermore, unless CO2 emissions are mitigated, the Southern Ocean krill population could collapse by 2300 with dire consequences for the entire ecosystem.