When the English settlers of Jamestown, Virginia, sailed into Chesapeake Bay in 1607, the first thing they did was plant a cross on the shore. They may not have had the same kind of focused religious mission as the Puritans of New England, but Virginians cared about things of the spirit.

As typical English people, the Virginia colonists were stridently Protestant. They were products of the warring worlds of the Reformation. Roman Catholics were the great imperial and religious enemy to most English Protestants. But the recent discovery of a Catholic reliquary (devotional box) in the grave of an early Virginia leader suggests that the colony’s religious story may have been more complicated than we knew.

The site of the Jamestown colony has become arguably the most exciting archaeological dig in America over the past couple of decades. Scholars once assumed that the James River had long since covered over the site of the original Jamestown fort. But in the 1990s, renewed excavations revealed that the fort’s remains were still on land, just waiting to be dug up. The new dig has produced stunning and tantalizing evidence about life at Jamestown.

In 2011, Jamestown announced that it had discovered the foundations of the fort’s church, likely the first Protestant church ever built in America. That church also hosted the most famous wedding of the American colonial era, between John Rolfe and Pocahontas.

Now excavators have unearthed the graves of several of the earliest colonists, including the Reverend Robert Hunt, who performed one of the first Anglican Communion services in America in 1607. More controversially, the grave of Captain Gabriel Archer, one of the colony’s early leaders, yielded a ...

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