The 17th Century saw the estate of Balgonie in the hands of the Covenanter and mercenary Sir Alexander Leslie. He was created 1st Earl of Leven by Charles I in an attempt to placate him but he nevertheless led an army that defeated the king at Marsden Moor. Later in the century a branch of the Balfour family bought Balbirnie and a link between the place and that family has lasted down to the present day.
Religious strife continued to tear the country apart for the rest of the century and Markinch ministers were regularly falling in and out of favour with the authorities, depending on the strength of their Episcopalian or Presbyterian sympathies.
Charles II granted Markinch the status of a Burgh of Barony in 1673, linked to the title of John Law, a firm royalist at that time who held the estate of Brunton and Dalginch. His coat of arms portrayed two red cockerels and the bird came to be displayed on the town's heraldic shield (see above). The motto "Constant in Faith" (Constans in Fide) proved to be over-optimistic because, within less than 20 years, the Episcopalian regime of Charles had been supplanted by William of Orange. William's staunch supporter, Lord Melville, a descendant of the Moulray family's old adversary, Melville of Raith, acquired Markinch and the Brunton and Dalginch Barony for his son David. Within a few years, the entire landholding fell into the hands of the Earldom of Leven through a marriage contract between the Leslies and the Melvilles.
By now Markinch had the right to trade and prospered thanks to the weekly fair. More houses were built, mostly thatched and huddled around the kirk next to the market cross. Almost all of these, once recognisable by their steep, often crow-stepped, roofs, have now been replaced by later Georgian and Victorian buildings.