The 16-year-old was assaulted in dark toilets at Fenelon-Notre Dame, a private Roman Catholic school in the Atlantic port city.
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Investigators hope to find a match for DNA traces found on her clothing.
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No such mass testing has been done before at a French school, AFP news agency says. The test is voluntary.
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Saliva samples will be taken from 475 students, 31 teachers and 21 other adult males who were on the premises at the time.
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While the testing, by plain-clothes police, is voluntary, any male refusing to take part could come under suspicion.
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Two classrooms are being used for the collection of DNA, which is due to end on Wednesday. The school has nearly 1,300 pupils in total.
All the DNA samples testing negative will be destroyed, AFP reported, quoting local prosecutor Isabelle Pagenelle.
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