Since 1259 the properties of the House of Brancion were taken over by the dukes of Bourgogne. These included the villages of Brancion,, La Chapelle-sous-Brancion, Collonges, Nogent, Martailly, Balleure, Charcubles, Chaux et Corcelles, Cussy, Dulphey, Fragnes, Royer, Mancey, Chissey, Vers, Culey, Prayes. At the head of the domain was a "captain" who represented the duke of Bourgogne. A magistrate of the court of Brancion and a forest master looking after the woods and the lakes assisted him. In 1376 Huguenin Plumeron, a wolf hunter presented him the front paws of six wolves and six she-wolves he had captured.
On All Saints Day in 1365, two "trappers" accompanied by six dogs caught, twelve otters in the lakes. The different "captains" looked after the maintenance of the buildings and turned the castle into "a strong and well maintained fortress".
As soon as the feudal system started, the lords themselves exercised justice but when more legal procedures replaced fights and tortures (water and fire ordeals) they appointed justice officers, the so-called “provosts”, who exercised justice in their name. The provost of Brancion lived in Balleure in the house called "La maison de la Prévôté". The land around, the meadows and the vineyards, belonged to the house. We know of several provosts like Denizot from the beginning of 1259; in the 16th century Jean de Digoine and Edme de Jordanne; in the 18th century George de Bauffremont and Hugues de Saint-Julien ; in the 19th century François-Emmanuel de Naturel.
The War between the Armagnacs and the Bourgignons
It started in the first years of the 15th century and lasted more than 25 years bringing destruction and desolation to Bourgogne. From 1409 onwards, Brancion had permanent troops. The fortress, defended by the illegitimate child of Chantemerle, was severely menaced in 1423 but Chantemerle thwarted the Armagnacs' plans. There were other threats in 1431, but then the "Traité d'Arras" in 1435 ended the war. Although the peace treaty was signed, there were still troubles: in 1443 the war mercenaries formed small gangs under the name of "Ecorcheurs" (skinners) and looted all over Bourgogne. The illegitimate child of Chantemerle informed the administration of Dijon that because of several unfruitful and dangerous years, some of the villages (e.g. Charcubles) had been abandoned. Finally, a year later, the "Ecorcherie" was finished and prosperity started to come back. The duke of Bourgogne, Charles le Téméraire died at Nancy in 1476. Louis XI attached the dukedom of Bourgogne to the Crown of France which meant that the "Châtellerie Ducale" became Châtellerie Royale".
Louis XI and Charles VIII handed it over for life, to a succession of lords selected by them, later on to farmers and from 1548 to appointed lords. They signed an agreement in which the King gave up his rights to one of his domains in exchange of the interest paid to him. The first contract was signed by Branges, Lessard, Saint Trivier and his wife Francoise de Polignac. The Châtellerie of Brancion stayed in the family de Lugny and de Baume-Montrevel until 1759. The next appointed lord was René Molineau who was a lawyer at Parliament in Dijon. After him came Antoine Prost de Royer and his nephew M. de Narboud. During the Revolution of 1789 the castle became nationalised.
The Religious Wars
At the beginning of 1562, during the religious wars, the Huguenots plundered the churches of Chalon, Mâcon and Tournus. The clergy of Tournus had to seek refuge in Brancion. Up to 1585 there were only a few serious incidents in that area. Brancion stayed in a state of alert because of some very complicated military operations around the castle of Cruzilles. On June 17, 1594 the King ordered Alphonse d'Ornano to "sort out" Brancion which had been taken by the members of the "Ligue". Its soldiers seized the village on June 21, "par le moyen de pétards et escalades" (with fireworks and climbing) and tried to besiege the castle without results. However, on October 7, 1594 one of Colonel Ornano's lieutenants, Captain La Folie, took it by surprise.
"L'Edit de Nantes" put an end to the religious wars. During these years of agitation, epidemics, starvation and different calamities hit Brancion. In 1573 caterpillars attacked the grain reservoirs in the area of Brancion. "les trémis furent endommagées par les chenilles que l'on excommunia du côté de Brancion".
The following year the pest decimated the population. Philibert Giraud, a notary of Brancion, went to live in Martailly for a certain time because of the bubonic plague. "pour raison de danger de peste qui regnoit lors au bourg de Brancion"