The painting, by an unknown but accomplished artist, showed the Queen clasping a bunch of roses when it first came to the National Portrait Gallery. But the roses are fading with time, and what they were painted over is now showing through.
There is a lot of mystery about the work, but researchers believe the fashion of the clothes suggests it was painted in the 1580s-90s, and it also appears to have been painted over an unfinished work, possibly by a different artist.
It is not known why Elizabeth would have been painted holding a snake (or why it would have been painted over - though that may seem less surprising). But her jewellery did include serpent emblems, though her portraits did not.
Serpents can be used to represent positive attributes such as wisdom - hence their use as the traditional symbol of medicine - but in the Christian tradition the main association is with the defiance of God in the Garden of Eden.
The story and theories of this painting and three others will appear in a new exhibit at the National Portrait Gallery: "Concealed and Revealed: The Changing Faces of Elizabeth I"
It will appear from Saturday March 13 until the autumn.