An ancient seed that germinated after being recovered from the rubble of King Herod's pleasure palace has been dated as 2,000 years old, smashing the record for the oldest seed ever grown.

The seed was among three recovered during excavations at Masada, an imposing 2,044-year-old clifftop fortress on the edge of the Judean desert overlooking the Dead Sea.

Researchers planted the seed three years ago after treating it with hormone-laced fertilisers. To their surprise, it germinated and began to grow. The plant, dubbed the "Methuselah tree" after the oldest character in the Bible, now stands 1.5m tall.

Dates were such an important export from ancient Judea they were depicted on coins and came to symbolise the region. According to the historian Josephus, miles and miles of hand-cultivated date forests stretched from the Sea of Galilee to the Dead Sea.

The palm two years after it germinated from a 2,000-year-old seed. Photograph: Guy Eisner/Science Magazine

Writing in the journal Science, a team led by Sarah Sallon, director of the Louis Borick Natural Medicine Research Centre at Hadassah Hospital in Jerusalem, reveal how they discovered fragments of the seed's shell clinging to the plant's roots when it was transferred to a larger pot. The fragments were sent to the University of Zurich, where researchers dated them to around 2,000 years ago.

The team had not been able to date the seed until then, because they were reluctant to cut pieces off for testing.

"The exceptionally dry and hot climatic conditions at Masada may have prevented it from disintegrating and preserved its viability, but this still says a lot about the ability of seeds to survive," said Sallon.

Until now, the record for the oldest seed to be grown was held by a group at the University of California who germinated a 1,300-year-old lotus seed recovered from a sacred Buddhist lake in China.

At Hadassah Hospital, Sallon investigates traditional, plant-based medicines. "Well over a third of Israel's 3,000 species of plants have been used in traditional medicine by Jews and Arabs for thousands of years," she said.

Her work has grown to include plants that have become locally extinct, as well as those which are still found in the wild. Extracts from date palms were traditionally used to treat chest infections, gastric problems and even heart conditions.

The ancient date palm differs from modern Moroccan, Egyptian and Iraqi varieties at around half of the 399 genetic markers the researchers looked at. It will be another couple of years before they know whether the plant can bear fruit – and so whether they will be able to cultivate it. "We hope that one day, we'll be able to breed it," said Sallon.

"The fact that seeds can survive for so long under the right conditions says a lot about conservation and ways to preserve seeds for future generations," Sallon added. "Thank god some seeds can survive, because the way we're busily cutting down everything on the planet, we're sure going to need them."