Officers from Market Drayton Safer Neighbourhood Team assisted the RSPCA with two warrants under the Protection of Badgers Act 1992.
Items relating to badger baiting were seized.
Constable Mick Sturland, of West Mercia Police, said: "Two addresses in Whitchurch were searched and two men were arrested and articles relating to baiting offences were seized.
"These warrants were executed after intelligence received by the RSPCA, who will interview the arrested men."
Badgers are protected animals, along with the setts or burrows they live in.
RSPCA press officer Lucy Cooper said: "The RSPCA joined police on two warrants which were executed in the Whitchurch area as part of an investigation into wildlife crime.
"Police have arrested two men. The investigation is currently ongoing."
Under the Protection of Badgers Act, in England and Wales it is an offence to intentionally kill, injure or take a badger, or attempt to do so.
Ill treatment of a badger, digging for a badger, intentionally or recklessly damaging or destroying a sett, or obstructing access to it, sending a dog into a sett, and disturbing a badger in its sett are also prohibited by the act.
But there are exceptions as licences to undertake some actions can be issued if it is justified, such as when a sett is on the site of a proposed road or housing development.
Undercover RSPCA inspectors have helped bring a number of successful badger digging cases before the courts. Some of these have involved the use of advanced forensic techniques including DNA evidence.