While Markale presents himself as being very widely read on the subjects about which he writes, he is nonetheless surrounded by controversy regarding the value of his work. Critics allege that his 'creative' use of scholarship and his tendency to make great leaps in reasoning cause those following the more normative (and hence more conservative) mode of scholars to balk. As well as this, his interest in subjects that his critics consider questionable, including various branches of the occult, have gained him at least as many opponents as supporters. His already weakened reputation was further tarnished in 1989, when he became involved in a plagiarism case, when he published under his own name a serious and well-documented guide to the oddities and antiquities of Brittany, the text of which had already been published twenty years before by a different writer through the very same publisher.

Also a source of controversy is his repeated use of the concept of "collective unconscious" as an explanatory tool. This concept was introduced by Carl Jung, but in modern psychology it's rejected by the vast majority of psychologists.

From Christian-Joseph Guyonvarc'h, Textes Mythologiques Irlandais, Rennes, Ogam-Celticum N°11/1 & 2, 1978, p. 39., Une critique détaillée de l'Ouvrage l'épopée celtique en Bretagne de Jean Markale (Irish Mythological Texts, A Detailed Critique of "Celtic Epics From Britain" by Jean Markale):

"Mr Jean Bertrand, a.k.a Jean Markale, styles himself as a professor of classical literature. He never says where he teaches; but [...] he cannot properly accentuate Greek, knows nothing of Latin [...] he doesn't know how many cases there are in Irish declension (sometimes he says two, at other times three) [...] Jean Markale very complacently quotes his own works in his later publications and, every time an Irish text is mentioned, he refers the reader to his 'Celtic Epics' as though that book included actual translations or constituted the most basic and essential reference on the matter. All this is, at best, a joke."

• The Celts: Uncovering the Mythic and Historic Origins of Western Culture (ISBN 0-89281-413-6)
• Montségur and the Mystery of the Cathars (ISBN 0-89281-090-4)
• Women of the Celts
• The Druids: Celtic Priests of Nature (ISBN 0-89281-703-8)
• Cathedral of the Black Madonna: The Druids and the Mysteries of Chartres
• King of the Celts: Arthurian Legends and Celtic Tradition
• The Epics of Celtic Ireland: Ancient Tales of Mystery and Magic
• The Great Goddess: Reverence Of The Divine Feminine From The Paleolithic To The Present

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