Compulsory microchipping and desexing of dogs and cats in South Australia will be in place by the end of the year after an amendment passed through State Parliament.

The Government predicts the new laws will reduce the number of pets being euthanased.

The amendments to the Dog and Cat Management Act were discussed for many years and the latest amendment is based on the findings of a citizens' jury, which urged that more effort be made to reduce the number of animals put down annually.

Environment Minister Ian Hunter said about 10,000 animals are euthanased each year.

"From my perspective that's 10,000 too many," he said.

"That means there's an issue with supply and clamping down on illegal puppy farmers is the first place for us to start."

There will be some exemptions for breeders, as well as security and working dogs.

Mr Hunter said the Government would look at ways to lower the cost of microchipping.

"We work with veterinarians and various animal agencies and we can actually microchip a large number at a very cheap cost," he said.

"We don't want anybody to feel this is going to be an impediment for them and of course the desexing part of the program only applies to new dogs once the law's been passed."

Dog and cat management board chairwoman Dr Felicity-Ann Lewis said the board was pleased with the amendments and they would not be retrospective.

"We are saying to people: Look, it's coming, so please get organised, do the right thing," she said.

Local councils will have the responsibility to enforce the laws.