Blood samples taken from birds as far afield as Sussex and the north of England were yesterday being analysed to see if they were lawfully captive or illegally taken from the wild.
Genetic DNA "fingerprinting" techniques were being used by experts at Nottingham University to find evidence of the birds' parentage.
All the species involved, peregrine, merlin, goshawk and Red Kite are specially protected under the Wildlife and Countryside Act. Police are believed to have been tracking a network of rare bird dealers for several months.
The Red Kite was one of three rare birds found at an address in Mid Glamorgan where trapping equipment and a rifle were also recovered.
A 47-year-old man was arrested and later released on bail pending further inquiries.
Several hawks were also found at the home of another breeder in West Glamorgan where a 39-year-old man was arrested.
Det Sgt Ian Guildford, South Wales police wildlife liaison officer, who co-ordinated the operation, said: "Birds of prey are subject to considerable illegal persecution. It is important that we send out a strong message to those involved that we will take steps to tackle these unusual crimes."
Roger Lovegrove, Wales regional officer for the Royal Society for the Protection of Birds, said: "We are delighted that the police are taking these types of offences seriously. The continuing persecution of birds of prey is of great concern to the public and ourselves."