Margaret II of Flanders (1202-1278) was countess of Flanders from 1244 to 1278 and countess of Hainaut from 1244 to 1246.

She was the younger daughter of Baldwin I of Constantinople, who was also count of Flanders and Hainaut, and Marie of Champagne. He left on the Fourth Crusade before she was born, and her mother left two years later, leaving Margaret and her older sister Jeanne in the guardianship of their uncle Philip of Namur.

After her mother died in 1204, and her father the next year, the now-orphaned Margaret and her sister remained under Philip's guardianship until 1208, when he gave their wardship to King Philip II of France.

In 1212 Margaret married Bouchard d'Avesnes, a prominent Hainaut nobleman. This was apparently a love match, though it was approved by Margaret's sister Jeanne, who had herself recently married. The two sisters subsequently had a falling out over Margaret's share of their inheritance, which led Jeanne to attempt to get Margaret's marriage dissolved. She alleged that the marriage was invalid, and without much inspection of the facts of the case Pope Innocent III condemned the marriage, though he did not formally annul it.

Bourchard and Margaret continued as a married couple, having 2 children, as their conflict with Jeanne grew violent and Bouchard was captured and imprisoned in 1219. He was released in 1221 on the condition that the couple separate and that Bouchard get absolution from the pope. While he was in Rome, Jeanne convinced Margaret to re-marry, this time to William of Dampierre, a nobleman from Champagne.

This situation caused something of a scandal, for the marriage was possibly bigamous, and violated the church's strictures on consangunity as well. The disputes regarding the validity of the 2 marriages and the legitimacy of her children by each husband continued for decades, becoming entangled in the politics of the Holy Roman Empire.

In 1246 king Louis IX of France, acting as an arbitrator, gave the right to inherit Flanders to the Dampierre children, and the rights to Hainaut to the Avesnes children. This would seem to have settled the matter, but in 1253 problems arose again. The eldest son, John d'Avesnes was uneasy about his rights, convinced William II, Count of Holland to seize Hainaut and the parts of Flanders which were within the bounds of the empire. William of Holland was, as emperor-elect, overlord for these territories, and also John's brother-in-law. A civil war followed, which ended when the Avesnes forces defeated and imprisoned the Dampierres at the Battle of Walcheren.