The village name comes from the English word 'marsh', describing the typical state of land in the area due to the high water table of the Aylesbury Vale. The affix 'Gibbon' derives from the family name 'Gibwen', being the manorial family here in the Twelfth century. In manorial rolls of 1292 the village was recorded as Mersh Gibwyne, though earlier (in 1086) it was known simply as Merse.
Anciently the village was the property of the abbey of Grestein in Normandy, France however in 1365 the village was seized by the Crown because it belonged to a foreign church. Later it was granted to a hospital at Ewelme in Oxfordshire.
Typical with other villages in close proximity to both Oxford and Aylesbury (see Brill or Boarstall, for example) Marsh Gibbon was largely wiped off the map in the English Civil War. A particular skirmish took place here in 1645, the groundworks of which still remain to this day at the manor house.
The hamlet of Westbury on the Oxfordshire border in this parish was given by King Edward IV to the Company of Cooks in London, though it has since been sold into private hands.
The parish church of Marsh Gibbon is dedicated to St Mary the Virgin.