Scotland Yard said the girl is not a line of inquiry and it has requested the sample to confirm statements made by New Zealand police the girl is not Madeleine.
A spokeswoman said: "This is not a line of inquiry, but just to corroborate what police in New Zealand are saying, we have requested DNA."
It was reported in New Zealand media the girl has been mistaken for Madeleine more than once, because she has a similar mark in one of her eyes.
Detective Senior Sergeant Kallum Croudis said: "Police will be sending a DNA profile to British police to confirm the identity of a girl who has been mistaken for Madeleine by a member of the public."
Madeleine was nearly four when she vanished from her family's holiday apartment in Praia da Luz in the Algarve on May 3, 2007, as her parents dined at a nearby restaurant.
A spokesman for the McCann family, Clarence Mitchell, said: "It is entirely a matter for Scotland Yard and the New Zealand police and Kate and Gerry (McCann) won't be commenting."