In the Middle Ages, the symbols of lily and fleur-de-lis overlapped considerably in Christian religious art. Michel Pastoureau, a historian, says that until about 1300 they were found in depictions of Jesus, but gradually they took on Marian symbolism and were associated with the Song of Solomon's "lily among thorns" (lilium inter spinas), understood as a reference to Mary. Other scripture and religious literature in which the lily symbolizes purity and chastity also helped establish the flower as an iconographic attribute of the Virgin. It was also believed that the fleur-de-lis represented the Holy Trinity.

In medieval England, from the mid-12th century, a noblewoman's seal often showed the lady with a fleur-de-lis, drawing on the Marian connotations of "female virtue and spirituality". Images of Mary holding the flower first appeared in the 11th century on coins issued by cathedrals dedicated to her, and next on the seals of cathedral chapters, starting with Notre Dame de Paris in 1146. A standard portrayal was of Mary carrying the flower in her right hand, just as she is shown in that church's Virgin of Paris statue (with lily), and in the center of the stained glass rose window (with fleur-de-lis sceptre) above its main entrance. The flowers may be "simple fleurons, sometimes garden lilies, sometimes genuine heraldic fleurs-de-lis".

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