The first time Bonnefontaine was mentioned in a written source, was at the beginning of the XIth century, when Geoffroy Chausseboeuf donated some of the land of Bonnefontaine to the abbey of Saint Florent in Saumur.
By the end of the XIIIth century, Bonnefontaine had been owned by the family of Saint Brice for three generations. In 1370 Guillaume de Porcon, son of Olivier de Porcon who was the companion of Bertrand du Guesclin, married Jeanne de Saint Brice, only heir of Bonnefontaine.

The Porcon family originally came from Saint Meloir des Ondes, close to Cancale. Arthur de Porcon was Chamberlain to the Duchesse Anne de Bretagne and captain of Fougères in 1488. During two centuries the Porcons remained the landlords of Bonnefontaine. In 1533 Françoise de Porcon is heir of Bonnefontaine.

She married Pierre Giffard de La Marzellière, who was raised at the court of King François I and first "gentleman" of his house. He was decorated with the medal of Saint Michel for his outstanding performance at the siege of Renty in the region of the Boulonnais in 1556. On the 5th July 1547 he obtained the right from King Henri II to change Bonnefontaine into a fortification. It was also him who ordered the construction of the south part of the castle including the tower.
In 1604 the daughter of François de La Marzelière inherited Bonnefontaine. A few years later in 1631 she married Malo de Coëtquen, son of one of the Orléans-Rothelin and great son of a Rohan-Guémené.

In these times the Coëtquen were also the Lords of Combourg (which is a few kilometers from here) and where they resided frequently. They were governors of Saint Malo. About 150 years later the famous phantom of Combourg with the wooden leg described in the book "les Mémoires d'outre tombe" by the great romantic author Chateaubriand (Count of Combourg) is no one else than Malo III de Coëtquen, Baron of Bonnefontaine (and son of Charlotte de Rohan Chabot).
1754 Bonnefontaine is sold by Louise-Maclovie de Coëtquen, wife of Emmanuel de Durfort Duc of Duras, to Jean de La Motte seigneur of Lesnage. After the death of his wife, Bonnefontaine was sold as national good in the year VII of the (French) Revolution as all legal heirs had fled the country.

Afterwards, Bonnefontaine changed owners several times until 1806, when it was bought by Guy Aubert de Trégomain. Being a friend of the legal heirs, the new owner bought Bonnefontaine with their agreement, and also compensated them. As a deputy of the Ille et Vilaine country (Part of Bretagne Region) under King Charles X, Guy Aubert de Trégomain was an ardent defender of the legitimist party who opposed king Louis-Philippe (Orléans familly). During the "intrigue of the West", lead by the Duchesse de Berry (King Charles X's daughter in law) who tried to overthrow the new king of the French at the profit of the Count of Chambord (grand son of Charles X), Guy Aubert de Trégomain was asked to take over the command of the army troops of Ille et Vilaine. 1858 Bonnefontaine is sold once again.

This time it is bought by the 26 years old Viscount François de Guiton (whose family is said to have been with William the Conqueror for the conquest of England in 1066) who was married to Françoise Hay des Nétumières. Twenty years later they started the important renovations which gave Bonnefontaine its actual aspect. The Vicountesse de Guiton died childless in 1910 and passed it on to her nephew, Jacques Marquis de Kernier. His daughter Beatrix Le Cardinal de Kernier brought it as dowry into the marriage with Count Léonor de Rohan Chabot. Since then Bonnefontaine has been in the hands of this family.