In 1663, James Dundas, First Lord Arniston (c.1620–1679), a judge and a Covenanter, suffered from the anti-Presbyterian Restoration policies. In 1679 he began to write the Idea philosophiae moralis but died before finishing the book. The Idea is a moral philosophical treatise in the tradition of Reformed scholasticism. The manuscript, only recently discovered in the Dundas family library, is an entirely new source for the study of Restoration Scotland. This paper presents what Dundas has to say about themes which are relevant to the seventeenth-century debates about tolerance regarding religion: Christian tolerance, conscience, natural law and the state. Dundas primarily understands tolerance as a Christian virtue helpful in the performance of moral duty. The paper suggests that a political concept of tolerance regarding religion is implicit in the Idea. Tolerance could be extended to those law- abiding Christians who subscribe to the moral-philosophical rational core of the divine and natural law, which grounds the unity of the state.