 Flora was born in 1722 at Milton on the island of South Uist in the Outer Hebrides, third and last child of Ranald MacDonald (d. 1723) and his second wife Marion.Her father was a member of the minor gentry, being tacksman and leaseholder of Milton and Balivanich; she had two brothers, Angus, who later inherited the Milton tack and Ronald, who died young.Her father died soon after her birth and in 1728, her mother remarried Hugh MacDonald of Armadale, Skye.