Pupils will be asked to consider creationism in science syllabuses being introduced from September.
In one GCSE biology paper by the OCR exam board, pupils are asked how organisms may have become fossilised. It says that "some species are better adapted to their environment and are more likely to survive. This is called natural selection".
It then asks teachers to "explain that the fossil record has been interpreted differently over time (eg creationist interpretation)".
John Noel, OCR science qualifications manager, said: "It is simply looking at one particular example of how scientific interpretation changes over time. The history of scientific ideas not only has a legitimate place in science lessons, it is a requirement of the new programme of study."
A similar reference is made by the Edexcel board. A draft scheme of work, published in January and intended to accompany new GCSE biology modules, asks pupils to discuss "creationist rejection of fossil evidence". It also asks pupils to consider theories, such as those of Darwin, Alfred Wallace, the British naturalist, and Samuel Wilberforce, the Victorian clergyman and former Bishop of Oxford, who once tried to insult a Darwin supporter by asking whether he was "descended from an ape on his grandfather's or grandmother's side of the family."
A spokeswoman for Edexcel said: "Creationism is not part of the national curriculum. We have included the debate on the issue in our draft scheme of work so students can discuss evolution and the evidence for it. But the creationism argument is not part of the assessment process for science."