The RSPCA project, which will cover England and Wales, is the first of its kind for a wild species.
It is hoped the database will help bring successful prosecutions against people who dig and bait the animals.
DNA can already be taken from a crime scene but there has been no reference database to prove the evidence - such as hair - is actually from a badger.
Experts hope to take around 400 samples from across the country to represent the badger population.
Insufficient evidence
The RSPCA has commissioned Wildlife DNA Services Ltd to set up the database of hundreds of badger samples.
Barry Fryer, chief superintendent at the Special Operations Unit at the RSPCA, said: "The database should significantly improve our chances of successfully prosecuting diggers and baiters.
"In the past, we have been unable to proceed with cases through insufficient evidence linking the defendants to particular badgers.
"With the extra supplementary evidence the DNA profiling will provide, we are confident that the cases we put forward will withstand the scrutiny of a court of law."
Techniques developed
DNA samples of badger hair, blood or faeces can be taken from a crime scene.
Dr Rob Ogden, of Wildlife DNA Services, said: "At present the human DNA profiling system used to help criminal forensic investigations makes use of large databases.
"Our aim is to build up an equivalent database for badger DNA which will assist the RSPCA in proving matches and securing prosecutions."
Genetic techniques for identifying individual badgers have already been developed.
'National map'
These profiles have been successfully used to identify individual badgers within three social groups with a 99% success rate.
When enough samples are collected, scientists will begin profiling and recording them to form a national map of profiles from badger social groupings.
RSPCA Special Operations inspectors have been given DNA testing kits which they will use to collect samples for the database.
In 2003, the RSPCA received 241 complaints of badger digging in the UK.
Under the Protection of Badgers Act 1992, it is illegal to interfere with a badger sett.
The maximum sentence is six months' imprisonment and a £5,000 fine.