The cases were re-opened after officers heard tapes seized from the American university, the BBC understands.
The murders being re-examined are those of John Benedict Devine in July 1989 and John Joseph O'Hara in April 1991.
No-one has ever been charged in connection with the two murders.
It is the first time loyalist killings have been investigated as a result of details in the Boston tapes.
Police say the two men were killed simply because of their religion.
Mr Devine, a 37-year-old father-of-three, was shot in front of his 13-year-old son at his home in Fallswater Street in west Belfast.
Mr O'Hara, a father-of-five, was working as a taxi driver when he was shot in Dunluce Avenue in south Belfast in April 1991.
Police have said they have new information that could help them to catch the killers.
"As a result of information we have recently received, we believe we are now in a position to progress both of these investigations.
"However, we need the help of the public," said Det Insp Neil McGuinness.
The Police Service of Northern Ireland will not comment on the nature of the new information.
But the BBC believes the decision to re-open these cases was taken after detectives listened to tapes seized from Boston College in recent months.
Dozens of former paramilitaries, most of them republican, gave interviews to university researchers compiling an oral history of the Troubles.
They did so on the understanding that the tapes would not be made public until after their deaths.
But police took legal action and were granted permission to access some of the recordings.
It is understood police believe information contained on some of the seized tapes could help them identify those responsible for these two killings.
Detectives are now trying to find other supporting evidence.
They have appealed to anyone with information about the killings to come forward.
Police are re-investigating the murders of two Catholics because of information from interviews about the Troubles by former loyalist paramilitaries for a history project by Boston College.