Early origins
His grandfather was Sir John Wyndham (died 1573) of Felbrigg (second son of Sir Thomas Wyndham (d. 1521) by his first wife Eleanor Scrope, daughter and heiress of Richard Scrope of Upsall Castle, Yorkshire) who inherited Orchard, Somerset from his wife Elizabeth Sydenham (d. 1 January 1571), daughter and co-heiress of Sir John Sydenham of Orchard, Somerset.
The ancestry of Sir John Wyndham is illustrated by the heraldic achievement shown on his monument in Watchet Church. It consists of a crest: A lion's head erased within a fetterlock or, a crest formerly belonging to the Felbrigg family of Felbrigg, Norfolk, Felbrigg Hall having been the second earliest known home of the Wyndham family (alias de Wymondham which originated at the manor of Wymondham in Norfolk), and nine quarters as follows:
1st & 9th: Azure, a chevron between 3 lion's heads erased or (Wyndham);
2nd: Azure, a bend or (Scrope), the paternal arms of his great-grandmother Eleanor Scrope (d. circa 1505), daughter of Sir Richard Scrope (1442–1485) of Upsall Castle, Yorks;
3rd: Argent, a saltire engrailled gules (Tiptoft), the paternal arms of Margaret Tiptoft (d. 1402 or 1431), wife of Roger Scrope, 2nd Baron Scrope of Bolton (1348–1403) (from whom Eleanor Scrope (d. 1505) was 4th in descent) and co-heiress of her father Robert de Tibetot, 3rd Baron Tibetot (d. 1372) of Nettlestead, Suffolk;
4th: Argent, a chevron between 3 rams passant sable a mullet for difference (Sydenham of Orchard Sydenham, later Orchard Wyndham);
5th: Argent, a fess between three men's legs couped sable, canting arms of Gambon of Moorstone in the parish of Halberton, Devon. Moorstone was an estate listed in the Domesday Book (1086) and in 1406 the Gambons were licensed by the Bishop of Exeter to have a private chapel in "their mansion of Morston". Substantial remains of the mediaeval manor house survive. Tempore Edward IV (1461–1483) Elizabeth Gambon the heiress of Moorstone, married John Sydenham of Orchard, which eventually brought the estate to the Wyndhams, who still owned it c.1630.
6th: Gules, a chevron between 3 roses argent (Wadham);
7th: Argent, on a chief gules two stag's heads cabosed or (Popham of Huntworth, North Petherton, Somerset, from which family the Wadhams inherited Ilton in Somerset where they built their seat of Merryfield.
8th: Argent, a chevron sable between three escallops gules (Pollard of King's Nympton, Devon.