Sandy Hamilton, 35, and Kevin James McKinley, 46, both of Larkhall, South Lanarkshire, were pulled from the water off the Galloway coast on Sunday.
BBC Scotland understands that both men were suspected by the authorities of involvement in the illegal puppy trade.
Mr Hamilton also faced trial over the deaths of two people in a road crash.
He was accused of causing death by dangerous driving after a head-on crash killed 85-year-old Giovanni Coppolaro and his wife Maria, 83, from St Ives, Cambridgeshire, in July 2015.
Mr Hamilton and Mr McKinley were reported missing on Saturday evening after failing to return from a boat trip from Port Logan, Wigtownshire.
Police confirmed on Sunday that their bodies had been recovered from the Irish Sea.
Officers are still trying to determine the circumstances surrounding their deaths.
BBC Scotland has learned that both men were known to the authorities in connection with the illegal trade of puppies from the Republic of Ireland.
A major route for the trade sees vehicles transporting puppies across the Irish sea by ferry into Scotland.
A BBC Panorama investigation into the trade - Britain's Puppy Dealers Exposed - was broadcast last year.
The programme obtained footage which showed Sandy Hamilton being stopped in September 2015 on a ferry from Northern Ireland.
A concealment of puppies was found in the boot of his car and on that occasion he was allowed to continue on his journey and keep the dogs.
The stop was carried out by the Scottish SPCA as part of Operation Delphin.
This multi-agency initiative, which includes Stena Line, Police Scotland, Trading Standards and HM Revenue and Customs was set up to tackle the puppy trade business and protect the welfare of puppies and their breeding.
It is now believed that Mr Hamilton and Mr McKinley may have been on their way to collect more puppies in a speedboat at the weekend when the fatal accident happened.
BBC Scotland understands that Mr Hamilton's body was recovered, along with a substantial amount of cash.
Police Scotland would not comment.
A Scottish SPCA undercover inspector told the BBC: "Puppy trafficking has been monitored for some time under Operation Delphin and we have identified a particular route between Scotland and Ireland.
"Operation Delphin has gained success tackling the illegal trade involving puppy trafficking in an attempt to improve animal welfare.
"We have seen the perpetrators develop more elaborate ways to source puppies undetected."
Mr Hamilton was due to stand trial on the death by dangerous driving charge in July 2017.
Mr and Mrs Coppolaro had been travelling in a Jaguar car on the A73 in North Lanarkshire when it was hit by a Volkswagen Golf being driven by Mr Hamilton.
He had denied overtaking a lorry on a bend when it was unsafe to do so.
Mr Hamilton was also accused of driving without insurance.
Two men who died in a speedboat accident off the west coast of Scotland at the weekend were suspected puppy smugglers, it has emerged.