The two dead animals - one female and one male - were found dumped at the side of the road between Whitsome and Hilton Farm.
Both had suffered broken necks, with the strength of the wire traps nearly beheading one of the badgers.
Police who attended at the scene sent the bodies for examination in Edinburgh, where it was revealed their injuries had been sustained by snares, wire nooses intended to kill foxes and rabbit's by land owners.
However, it seems both badgers were killed - an illegal act in Scotland - and then left at the roadside to seem like a road kill.
Ian Hutchison, Species Protection Officer for the charity Scottish Badgers, said : "We've known of badgers being dumped at roadsides for a while but this is the first incident we have found.
"We lose hundreds of dead badgers on roads but when two were found together we were suspicious.
"We are constantly assured by land managers that animals will not be killed by snares but it continues to happen.
"Badgers put up a tremendous fight (when caught in a snare) - they dig, fight and then sometimes hang themselves on fences.
"It takes a while for them to die so it is a horrible death.
"These badgers had broken necks, with one of them almost decapitated.
"We know a snare has had a badger because they spin around and create a distinctive pattern on the ground - like a doughnut shape."
Admitting badgers can be pests to land owners, Mr Hutchison still does not believe that snaring is the answer to controlling them.
He said: "There are a lot of badgers in the Borders - some say there are too many - but they are protected by law.
"There are legal means to take badgers away but this has obviously not happened here.
"I am not one of those that think they are cuddly pets - they can cause problems if sets spread from field edges but there is a legal remedy and this isn't it."
Scottish SPCA have not been involved in the investigation into the deaths of the badgers but spokesperson Doreen Graham indicated the Borders wide variety of wildlife is attracting more crimes against the region's animals.
She said: "The Borders is rich in wildlife but some people view the wildlife as a problem.
"We have dealt with quite a few cases of wildlife crime in the Borders from poisoned golden eagles to illegal traps.
"What is quite disturbing about this incident is that the bodies were left at the side of the road to seem like an RTA (road traffic accident).
"The SSPCA's view is that a government ban is needed (on snaring).
"In this day and age there are much more modern ways of dealing with animals than essentially using a piece of wire that is like getting caught in a cheese grater."
Snaring is still allowed in Scotland - though the killing of badgers is not - after the Scottish Government Minister for Environment, Mike Russell MSP, refused to ban the traps earlier this year.
Mr Russell said the devices were vital for pest control and helps farmers to protect their animals and crops.
But Advocates for Animals campaigns director Ross Minett rejects Mr Russell's conclusion and believes the latest death by snare in Berwickshire strengthens their case for an outright ban.
Mr Minett also thinks there are alternatives to snaring for keeping pests under control.
He said: "It is a cruel and inhumane way to die.
"The Environment Minister Mike Russell ruled for a review of regulations which we think will not work - we want a ban.
"There are less inhumane ways of controlled animals such as shooting but snares are cheap and efficient - a gamekeeper can lay hundreds of snares at a time.
Until they are seen for what they are – lethal, indiscriminate and unacceptable – tragic incidents of this type will keep occurring."
Nine badgers have been killed by snares in Scotland so far this year, with that number possibly rising to 15 as an investigation into the deaths of six of the animals is currently ongoing.
Two badgers have already been the victims of the wired traps in the Scottish Borders, one found at Cardrona and the other at Edgerston, Jedburgh.
A spokeswoman for Lothian and Borders Police confirmed that the division's wildlife liaison officer had been involved with the case and that their investigation into the deaths was ongoing.
She said: "On May 2, two dead badgers were found at the road side between Whitsome and Hilton Road.
"Examinations revealed they had been killed at snares."