The arrests followed raids in East Kent on two homes, one business address and a dive boat.
The raids were carried out by police officers from Kent and Essex, archaeologists from English Heritage and officials from the Maritime and Coastguard Agency, including the Receiver of Wreck.
At one address, accompanied by a BBC TV news crew, their biggest find was a large, two-tonne bronze cannon, believed to be a 16th century Dutch piece from the London and worth an estimated £30,000.
In the televised report it appeared to be in a clean condition and sat partially immersed in a tarpaulin-covered trough of water in a back garden.
Other artefacts found at the same address included deck fittings, lead, china, glass and portholes. In all about 150 items, suspected to have come from a number of wrecks, were seized.
According to the BBC the arrested men, aged 54 and 44, have been released on bail after being interviewed at a Kent police station.
Police are examining materials including business records and computer images, while archaeological experts will be working to establish firmly the provenance of all the finds.
English Heritage will then be able to confirm whether any offence has occurred under the Protection of Wrecks Act, in relation to protected material.
The Receiver of Wreck, meanwhile, will be establishing whether any offence has occurred under the Merchant Shipping Act, in relation to the non-reporting of finds.
The arrests follow the February launch of the Alliance to Reduce Crime Against Heritage (ARCH), intended to harden up enforcement of heritage law.
Under ARCH, various authorities are working in a more symbiotic way to improve investigative efficiency.
HMS London, which sank after blowing up off Southend in 1665, was protected in October 2008.
Five bronze cannon had been recovered from the site without archaeological investigation the previous summer.
This was one of several non-archaeological salvage operations known by English Heritage to have taken place at the site.
The company which recovered the cannon for commercial gain had acted legally in that the wreck was not protected and the recoveries were reported to the Receiver of Wreck.
The cannon were from both England and Holland. Dutch cannon, captured during the first Anglo-Dutch War of 1652-54, would feasibly have been refitted aboard London and other British warships.
The historical value of the ship’s bronze armament was indicated by Charles Trollop, the ordnance expert who examined the cannon.
“Very few bronze guns survive,” he said. “They mostly went into the melting pot.”
In the year of the London’s sinking, bell divers recovered about 18 of its cannon. Another six or so were raised before the end of the century.