Dubbed the "Unknown Wreck off Eastbourne" since it was discovered near the seaside resort, the Klein Hollandia was identified through research by the agency and Dutch counterparts working with nautical archaeologists.
The wreck, which is 32 metres (103 feet) underwater, was found by a local dive operator in 2019.
"The condition of the wreck is remarkable and could offer a wealth of information about how 17th-century Dutch ships were built and the activities of the warship during its final voyage," Historic England said in a statement.
It said material found on the seabed included "much of the wooden hull, cannons, Italian marble tiles and pieces of Italian pottery".
Historic England, the Cultural Heritage Agency of the Netherlands (RCE) and the Nautical Archaeology Society examined material found on the seabed, tree ring analysis of wood samples and archives to identify the ship.
The Klein Hollandia -- a veteran of all the major battles of the second Anglo-Dutch war from 1665-7 -- sank carrying a cargo of marble tiles for use in building high-status homes.
It was en route from the Mediterranean to the Netherlands when it was attacked and badly damaged by an English squadron.
After its commander was killed in action, the English boarded the Klein Hollandia but it sank with both English and Dutch sailors on board, according to Historic England.
The surprise attack is believed to have contributed to the start of the third Anglo-Dutch War, part of a series of mainly naval conflicts between 1652 and 1784 fought over trade and overseas colonies.
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