The fossils suggest that fungus may have evolved from under the deep sea rather than land.
Drilled from rocks that were once beneath the seafloor, the fossils resemble living fungi and could push back the date for the oldest fungi by one to two billion years.
If not a fungus, the organism could be from an extinct branch of life that has not been described before, scientists say.
"The deep biosphere where the fossils were found represents a significant portion of the Earth, but we know very little about its biology and even less about its evolutionary history," said Stefan Bengtson of the Swedish Museum of Natural History in Sweden who led the research team.
There is a "clear possibility" that they are the world's oldest fossil fungi - twice as old as generally accepted in the fossil record, Bengtson was quoted as saying by the 'BBC News'.
The fossils were collected by drilling into ancient rock formed from lava that was once beneath the sea bed in what is now South Africa.
Known as the Ongeluk Formation, the location was underwater at the time the organisms would have been alive, researchers said. The fungi may have colonised cavities of rock deep beneath the sea floor.
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