Dr Eiddwen Jones, 85, is the great-great-great-great-great-granddaughter of Thomas Jones, who she said was the first miller at Llynon mill in 1776.
He managed the property in the village of Llanddeusant, Anglesey, until he died in his nineties.
She said the windmill should be repainted in whitewash as it is a historical building, and traditionally "that's how the mills were".
The author, whose family moved from Anglesey to Flintshire 150 years ago, said she did not agree that the windmill was painted in the first place to celebrate the Eisteddfod.
She has visited the windmill several times throughout her life where Thomas Jones' name is painted inside, and said he "would have turned in his grave, I believe," if he had known about its new appearance.
Jones added that it looked "very impressive in its original colour" when driving towards it.
"It's been made fun of now rather than kept the fact that it was a historical building and that people have been working there for a couple of centuries," she said.
Holt said the mill can be hard to find for visitors, as it is not close to the A55 road.
But the new colours have sparked a lot of interest.
With winters especially proving difficult with fewer people coming, he added: "I have a duty to ensure the future of the mill for the next generation."
He apologised to the local authority, saying he "realises that they [the council] are only doing their job and I know that I have broken the rules".
But he added: "I'm struggling and the winter is hard, but painting the mill has attracted more visitors here and helped me pay the bills."
He is gathering the opinions of visitors to the mill this summer to make a case to the council.

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