Through the ages, the lily has been a lasting Christian symbol of purity, most frequently associated with the Virgin Mary. Through her it has been attached to Gabriel (from representations of the annunciation) as well as Joseph her husband. However, it can be found with Catherine of Siena, Clare, Euphemia, and Scholastica. There is an even longer list of male saints that includes Francis of Assisi, Dominic, Antony of Padua, and Philip of Neri (especially as he prays before the vision of the Virgin).
The origins of how the fleur-de-lys (“Flower of the Lily”) became associated with the French monarchy are so tied up in ancient legends that we will likely never know the truth. One legend says that it represent the lily that an angel–or even the Virgin Mary, herself–gave to Clovis (r. 481-511) when he converted to Christianity. Another story claims that Clovis adopted the symbol when waterlilies showed him how to safely cross a river and thus succeed in battle. Less fanciful stories have it that Clovis accepted the lily as the symbol of his post-baptism purity.
All of the Clovis/fleur-de-lys myths enter the historical record in the 12th century when the Capetian kings of France were burnishing the monarchy’s legend of being divinely anointed. In any case, there is no historical evidence that French monarchs officially adopted the symbol until the 12th century when either Louis VI (or perhaps Louis VII) became the first French king to use the fleur-de-lys on his shield.
Joan of Arc carried a white banner that showed God blessing the French royal emblem of the fleur-de-lys when she led troops into battle with the English. Not to be out-done in the war of symbolism, English kings used the fleur-de-lys on their own heraldry to emphasize their claim to the French throne. Indeed, it became such a powerful symbol of French royalty none of the Republics of France have adopted the symbol even after the distance of almost 2 centuries since its official use.
As a symbol of the French monarchy, doubt remains as to what meaning it conveys. The traditional view is that the three petals represent the Holy Trinity. Another reference would suggest that it signifies perfection, light, and life. One historian (Georges Duby) claims it represents the three classes of ancient France: those who worked, those who fought, and those who prayed. If you dig deep enough in the bowels of the Internet (and I don’t suggest you do), you will even find a theory that the three petals started out being three frogs of pre-baptized Clovis. One site credibly asserts that in its earliest incarnations, the fleur-de-lys wasn’t a lily at all, but the iris which was indigenous to Gaul and was often called a lily.