The new rules state that from 2013, all free schools in England must teach evolution as a "comprehensive and coherent scientific theory".
The move follows scientists' concerns that free schools run by creationists might avoid teaching evolution.
Sir Paul Nurse, president of the Royal Society, said it was "delighted". Sir Paul told BBC News the previous rules on free schools and the teaching of evolution versus creationism had been "not tight enough".
He said that although the previous rules had confined creationism to religious education lessons, "the Royal Society identified a potential issue that schools could have avoided teaching evolution by natural selection in science lessons or dealt with it in a such a perfunctory way, that the main experience for students was the creationist myth"."
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