John Bayntun is said to have married Joan Echingham, the eldest daughter of Sir William Echingham and Joan FitzAlan De-Arundel of Etchingham, Co. Sussex, with whom he had six children. Sadly there is no records of the death of Joan Echingham or the birth of her children. But some years later, Sir John remarried Katherine Payne, the daughter of Thomas Payne of Payneshay, Devonshire and the widow of John Stourton of Preston Plunkett, Somerset.

There is great confusion and uncertainty about this first marriage to Joan Echingham, as Joan's mother died in 1404. Even assuming that she died during childbirth, Joan would be at the very least 20 years older than John.

The eldest son, and heir, from this dubious marriage was called Robert Bayntun, who was born in 1439. This would have made Joan 35 years old and John Bayntun approximately 15 years of age at this time. John's date of birth is also uncertain and if we were to allow for error and perhaps assume that he could quite possibly be a couple of years older, there would still be a considerable age gap between he and Joan.

This is not entirely impossible, if such a marriage was arranged, but nevertheless it is not supported by any sound documentary evidence and therefore there are suggestions that Robert Bayntun may very well have been born to John's second wife, Katherine.

This would seem more likely, as Katherine Payne was the third wife of John Stourton, who died on the 10th November 1438. If she married, John Bayntun shortly afterwards, then it is likely that Robert Bayntun (born 1439) could be the son and heir from this marriage and the other children could also be from this marriage.

Because Robert was named heir to his father, it would not necessarily be the case that he was the first born. Some of his other brothers may well have been born before him to Joan Echingham but had died before their father. While there is also no absolute proof that Joan Echingham was the mother of any of Sir John's children, she was named in the Great Pedigree and Visitation of 1623, and it is safe to presume she could have been the mother of some of them, unless proven otherwise.

John Bayntun was Knight of the Shire for Wiltshire in 1449 and was appointed a Commissioner to assist the Duke of York to put down the Devon riots in December 1455. He was also the owner of a property, very likely an Inn, called Le Abbay in Culver Street, Salisbury about this time.

A document dated September 20th 1450, lists John Bayntun, knight; Robert Hungerford, knight, Lord of Hungerford; Robert Hungerford, knight, Lord of Molyns; William Beauchamp, knight Lord of Saint Amand; and others, as Commissioners, appointing them to call together all the King's lieges of whatsoever estate, rank and condition to go with them against the traitors and rebels in Wiltshire and counties adjacent and to arrest and judge the same.

There is a mention of Sir John Bayntun in a Tourn (a type of court roll for the local business of the village of Faulston), dated 1465, relating to arable land, lately John Bayntun knight and Michael Kymer, fee tenant. Presumably Kymer had taken over some land previously farmed by John Bayntun but had not paid his rent.

Sir John Bayntun died on 20th June 1465 and his wife Katherine remarried again for the third time to William Caren MP of Taunton, Somerset, Steward of Shaftesbury Abbey and Agent for the Duke of Somerset in 1468.

There is no record of the burial place of Sir John, but it is thought he and his family before him, may have been buried in a square field, known as Chapel Close, which might have been either the site of a Chapel or a field attached to the Chapel which was next to Faulston House. There are no visible signs of any graves today, unless buried beneath the ground.

Katherine died in 1473 and at this time the Manor of Faulston and the Manor of Tollard Lucy were passed onto her son Robert. She had inherited the Manor of Preston Plunkett at the time of her first husband's death and when she died it was distributed among her children from her marriage to John Stourton.

When Sir John Bayntun died, he was succeeded by his eldest son and heir Robert Bayntun