The mystery girl from the 1800s whose body was found beneath a San Francisco home last year, her body entombed in a small lead and bronze coffin and her well-preserved hands clutching a single red rose, has been identified.

The nonprofit Garden of Innocence project said Tuesday that the child — who surprised not only the work crew that stumbled upon the casket, but also city officials who thought the bodies in a 19th century Richmond District cemetery had all been moved — is Edith Howard Cook.

Edith was a month and half short of her third birthday when she died Oct. 13, 1876, according to researchers working with the Southern California’s Garden of Innocence. The cause of her death? Probably severe undernourishment caused by an infection, the researchers said.

The team had been working to identify the girl since her body was discovered last May during a home remodeling project near Lone Mountain.

“It was a light at the end of the tunnel finding out who she is,” said Erica Hernandez, a project spokeswoman.

The researchers, who included staff at UC Berkeley, UC Santa Cruz and UC Davis, located records from the old cemetery that was run by the Independent Order of Odd Fellows until about 1902, when the graves were relocated to Colma.

Although the paperwork was “unorganized,” Hernandez said, the team was able to cross-reference plot records with old newspaper obituaries and get an idea of who the young child might be.

Once it concluded that Edith was probably the girl, the team tracked down living relatives for a DNA sample to verify their finding. That confirmation came when a sample from Edith’s hair matched that of Peter Cook, a descendant of her brother, who lives in Marin County.

Edith Howard Cook was the second child and first daughter of Horatio Nelson and Edith Scooffy Cook. Peter Cook is descended from Edith’s older brother, Milton H. Cook.

Edith’s family was believed to be of decent means, having buried the child in a relatively expensive metal casket 37 inches in length, with two viewing windows on the lid.

Her skin and hair, as well as her burial flowers, were well preserved. She was one of about 30,000 people with graves at the old Odd Fellows Cemetery. Why her remains weren’t transported to Colma around 1920, when the city wanted to make room for the living, remains a mystery.

Her coffin was found when workers remodeling a home smacked it with a shovel. The homeowner, Ericka Karner, swiftly contacted the city, but the medical examiner’s office said that because the coffin was on private property, it was hers to deal with.

Garden of Innocence stepped up to help Karner respectfully dispose of the remains. On June 4, Edith was reburied at Colma’s Greenlawn Memorial Park. About 140 people attended the service.

Another memorial service is scheduled for June 10 at the burial site to recognize her newfound identity.

Kurtis Alexander is a San Francisco Chronicle staff writer. Email: kalexander@sfchronicle.com Twitter: @kurtisalexander