The Doomsday Survey records that in 1066 'Hotone' was held by Earl Edwin and it was worth £8; by 1086 it had passed to Richard of Sourdeval, being Robert, Count of Mortain, tenant-in-chief, and it was valued at £5. During the first half of the 12thc Hooton was held by Ralph Paynel (or Paganel) and his son William, and the latter part of the name of the village derives from them.
There is no mention of a church in Domesday Book. The church was given to the Benedictine priory of Holy Trinity in York by its (re)founder Ralph Paynel around 1090-1100, a gift confirmed by King Henry I c.1100-1108. Ralph Paynel’s grandson granted the church to Nostell priory, but the grant appears to have had no effect, and between 1154 and 1181 he gave an interest in the church to Roger archbishop of York’s new foundation, the chapel of St Mary and the Holy Angels in York Minster. Moieties of the church were appropriated to Holy Trinity priory and to the chapel [Clay (1939), XII and nos. 1, 2, 4, 132].