Waters around Antarctica are becoming more acidic due to increased levels of carbon dioxide and are corroding the protective outer layer of swimming snails, found the study by a team of international researchers.
The situation is at its worst in polar regions because the gas is more soluble in cold water, the 'Daily Mail' reported.
Scientists have predicted that the average acidity of oceans across the planet will triple for the first time in 20 million years.
Scientists scanned shells collected from molluscs on the surface of the Southern Ocean with microscopes and found those from the most acidic regions were being dissolved across their entire length.
They blame the phenomenon on the mixing of deep water already rich in carbon dioxide with the surface being affected by atmospheric greenhouse gas.
"The impact of ocean acidification is already occurring in oceanic populations, long before some projected dates. Regional declines of pteropod populations may occur sooner than projected at present in Southern Ocean surface waters," Dr Geraint Tarling, of the British Antarctic Survey, Cambridge, said.
The destruction of this key group of molluscs, known as pteropods, spells potential disaster for the food chain.
Marine geologist Professor Justin Ries, of the University of North Carolina reviewed the findings published in Nature Geoscience.
"Despite their small size, pteropods are important food sources for predators at multiple tiers of the food chain, including zooplankton, herring, salmon, sea birds and even whales," he said.
"Without shells, pteropods would be defenceless against predation, which could cause their populations - and those of their predators - to collapse," he added.
"A decline in pteropod shell mass would also reduce the ballast available for sinking pteropods' inorganic and organic carbon to the deep sea, potentially disrupting the global carbon cycle," he said.
Laboratory tests suggest shell molluscs including clams, conchs and whelks will also be at increased risk.
Ries said that field and laboratory experiments show ocean acidification will impair the ability of corals, clams, snails, urchins and some calcareous algae to build their protective shells.
He said the corrosion of Southern Ocean pteropods documented in the study has yet to trigger a "butterfly effect" - the idea small changes in a system's initial conditions, such as the flapping of a butterfly's wings, may trigger large scale alterations in that system.
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