Kelly Thomas dropped to her hands and knees to peer at a tiny grave marker that barely poked above the soil at the Eliot Burying Ground, a centuries-old cemetery nestled behind an iron fence and stone walls in a dense neighborhood just off Nubian Square in Roxbury.

“This is the oldest stone in all of Boston,” said Thomas, who manages the city’s 16 historic cemeteries.

In a city where millions visit the graves of Revolutionary heroes each year, this small stone for 6-month-old Samuel Danforth, who died in 1653, is seldom noticed. But for Thomas, the resting place of an infant son of an early Roxbury minister evokes the distant past with a simple, meaningful eloquence.

“They were very unlike us, but in some ways the same,” Thomas said, gently tamping down the grass for a better look at three lines of carefully carved text.

The baby is buried in the earliest graveyard for Roxbury’s Colonial settlers, a triangular space of less than an acre that was established in the 1630s. It contains the remains of the Rev. John Eliot, who preached among Native Americans, and Colonial governors Thomas and Joseph Dudley, for whom Nubian Square was once named.

It’s a historic jewel that predates Roxbury’s annexation to Boston by more than 200 years. But walking among the artistry on its slate stones requires some effort. The iron gate is locked, and a high fence atop a stone wall discourages access.

“Eliot Burying Ground is locked to prevent vandalism and destruction of historic resources,” Thomas said of the site, which is on the National Register of Historic Places.

The cemetery is open to the public, but visits to Eliot, as well as nine other historic graveyards across the city, are by appointment only.

Most visitors to Eliot are there to conduct genealogical research on ancestors, Thomas said. Historic graveyards in the center of Boston, such as the Granary Burying Ground and King’s Chapel, attract exponentially more visitors but also bring greater concerns about safekeeping and maintenance.

“The primary function is as a burying ground, and that function has to trump all other concerns,” Thomas said. “You have to respect what the dead people want.”

A gravemarker restoration project recently wrapped up at Eliot, where 130 stones have been repaired by Daedalus, an art conservation company in Watertown. For owner Josh Craine, the stonework is fascinating.

“They’re amazing pieces of art and amazing pieces of American history,” he said. “They’re an important part of our shared cultural heritage and the people who were here.”

And they’re a testament to craftsmen who often worked in challenging, relatively primitive conditions with limited resources, historians say.

“They were just fantastically skilled,” Craine said. “You don’t get a lot of chances with it. You mess up, and you’re sort of stuck with it.”

Each slate marker is composed of multiple layers of stone, he said, and their repair often involves reattaching the carved facing to the layers behind it. Other fixes include filling small cracks with mortar, as well as simply cleaning the stone.

“To do it right, it takes a fair amount of time. It’s a couple of days to get one completely done,” Craine said. “To see what they did with what they had is really amazing.”

Thomas shares that fascination. As she walked among the stones, set on and around a small knoll topped by a lilac tree, she stopped before a poignant reminder of the myriad hardships of Colonial life.

There, in a row, were markers for four small children of the Pierpont family and their 32-year-old mother, all of whom died within a few years of each other. Carvings of skulls and wings top the stones.

“This is a wealthy family, and it illuminates something that was heartbreakingly common,” Thomas said. “It strikes me every time I come here."

The stones memorialize Sarah and Hannah Pierpont, both of whom died in September 1742; another Sarah, who died in March 1749; and Elizabeth, who was buried in May 1751. Beside them is their mother, Hannah, who also died in 1751.

Burials were discontinued at Eliot in the mid-19th century, and records for this graveyard at Washington and Eustis streets do not include the names or sites for an unknown number of slaves.

“They’re buried here, everywhere,” Thomas said.

The burying ground also was adjacent to the defensive works that Colonial soldiers built during the Revolutionary War, sealing off the narrow land bridge of Roxbury Neck from the British troops garrisoned in Boston.

Revolutionary soldiers took shelter behind the gravestones from incoming fire, and some are buried here.

“I try to imagine it,” Thomas said. “That’s what I like about this job. If you’re a history nerd, you come across nuggets like that, and you can live off that for several months.”

Preserving these “significant repositories of Boston history” remains important, said Candelaria Silva-Collins, chair of the George B. Henderson Foundation, which has approved two conservation grants for the Eliot since 2010, totaling $72,000.

Over that time, the city’s historic cemeteries have received $152,000 from the foundation, which seeks to enhance the physical appearance of the city, including its permanent public art, Silva-Collins said.

Thomas, who wore a Dorchester baseball cap this recent day, has cared for the city’s old burying grounds for 22 years. It’s a hands-on job in which the past is always present, something she treasures.

“I never thought I would be that person,” Thomas said, glancing around the Eliot. “But I can’t think of anything better.”

Brian MacQuarrie can be reached at brian.macquarrie@globe.com.

Work at Boston Globe Media