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Why two flags? A long and complex historic process caused confusion between two types of purple colour (a strong purple: colour with a hue between that of violet and red; and a light purple: colour with a hue between that of crimson and blue), and that is why it had to be claimed as regional ensign the light purple colour of Castilla banner. The confusion started when the royal army of Charles I defeated the commoners in the Villalar battle in 1521. At that moment the House of Austria arms will replace the old coat of arms and banner of Castilla y León.
With the passing of the time, the Austria's royal escutcheon made disappear the former and started the wrong association between the strong purple and the light purple colour. This will continue after the creation of some military units of "Royal Guards" during the reign of Philip IV, and during the XVIII and XIX centuries, by the Spanish Republicans of the I and II Republic: they also used this light purple colour as a symbol. We now know that historically the right thing to say is that the Castilla banner is crimson, and not purple.
The banner kept at the Colegiata de San Antolín, in Medina del Campo (Valladolid), from the beginning of the XVI century, was the model to create the Castilla y León banner, even they made some changes in the ornaments and figures. That design was carried out before the autonomic process, by the Valladolid Town Hall. Other Corporations followed its model in the next few months, and they accepted the double flag representation in the Committee that was writing the Statute of Autonomy Project. That way it was introduced and approved in the text.