The mummy was discovered in Egypt's Valley of the Kings burial ground in 1903 but was left unidentified at the site for decades, until two months ago when it was brought to the Egyptian Museum in Cairo for testing, said Egypt's antiquities chief Zahi Hawass.
"We are 100 percent certain" the mummy belongs to Hatshepsut, Hawass told The Associated Press.
Along with DNA probes, the scientific testing of a tooth found in a relic box containing some of the queen's embalmed organs was key to identifying the mummy as Hatshepsut's. The molar perfectly matched a gap in the jaw of the mummy.
A woman monarch who called herself a pharoah, dressed like a man and also wore a false beard, Hatshepsut ruled during the 15th century B.C., weilding more power than two other women of ancient Egypt, Cleopatra and Nefertiti. But when her rule in the 18th Dynasty ended, all traces of her mysteriously disappeared, including her mummy.
Another mummy, which had been in the Egyptian Museum for decades and was long believed to be the queen's wet nurse Sitre-In, was initially investigated as possibly being Hatshepsut herself.
Hawass and Culture Minister Farouq Hosni ceremoniously unveiled the two mummies, kept inside long glass cases draped in the Egyptian flag, at a press conference at the museum Wednesday.
The mummy identified as Hatshepsut shows an obese woman, who died in her 50s, probably had diabetes and is also believed to have had liver cancer, Hawass said. But her left hand is positioned against her chest, in a traditional sign of royalty in ancient Egypt.
DNA bone samples taken from the mummy's hip bone and femur are being compared to the mummy of Hatshepsut's grandmother, Amos Nefreteri, said Egyptian molecular geneticist Yehia Zakaria Gad, who is on Hawass' team.
While scientists are still matching those mitochondrial DNA sequences, Gad said Wednesday that preliminary results were "very encouraging."
Hawass has led the search for Hatshepsut since a year ago, setting up a US$5 million DNA lab in the basement of the Cairo Museum with an international team of scientists. The study was funded by the Discovery channel, which is to broadcast an exclusive documentary on it in July.
"This is a fantastic story of an ancient Egyptian queen but also a real scientific discovery," said Peter Lovering, from Discovery's production team.
Molecular biologist Scott Woodward, director of the Sorenson Molecular Genealogy Foundation in Salt Lake City, was cautious ahead of Wednesday's announcement.
"It's a very difficult process to obtain DNA from a mummy," said Woodward, who has done DNA research on mummies. "To make a claim as to a relationship, you need other individuals from which you have obtained DNA, to make a comparison between the DNA sequences."
Such DNA material would typically come from parents or grandparents. With female mummies, the most common type of DNA to look for is the mitochondrial DNA that reveals maternal lineage, said Woodward.
"What possible other mummies are out there, they would have to be related to Hatshepsut ..." Woodward said. "It's a difficult process but the recovery of DNA from 18th Dynasty mummies is certainly possible."
Molecular biologist Paul Evans of the Brigham Young University in Provo, Utah, said the discovery could indeed be remarkable.
"Hatshepsut is an individual who has a unique place in Egypt's history. To have her identified is on the same magnitude as King Tut's discovery," Evans told The Associated Press by phone from Utah.
Hatshepsut is believed to have stolen the throne from her young stepson, Thutmose III. Her rule of about 21 years was the longest among ancient Egyptian queens, ending in 1453 B.C.
Hatshepsut's funerary temple is located in ancient Thebes, on the west bank of the Nile in today's Luxor, a multi-collonaded sandstone temple built to serve as tribute to her power. Surrounding it are the Valley of Kings and the Valley of the Queens, the burial places of Egypt's pharaohs and their wives.
But after Hatshepsut's death, her name was obliterated from the records in what is believed to have been her stepson's revenge.
She was one of the most prolific builder pharaohs of ancient Egypt, commissioning hundreds of construction projects throughout both Upper and Lower Egypt. Almost every major museum in the world today has a collection of Hatshepsut statuary.
British archaeologist Howard Carter worked on excavating Hatshepsut's tomb before discovering the tomb of the boy-king, Tutankhamun, whose treasure of gold has become a symbol of ancient Egypt's splendor.