There are two sources which can be used for information on the various types of flags carried at Sedgemoor. Nathan Brooks gave details of the colours and standards he saw at the review at Putney Heath in 1684 and Sandford's Coronation of James II detailed those of the Household troops attending the ceremony. Brooks' description comes from the last year of the reign of Charles II and for the coronation of James, new standards were issued to the Household regiments and others changed their standards due to expansion and reorganisation.

With the exception of the Foot Guards and the Life Guards, the changes were due to an increase in the number of troops in the regiments of Horse as the identifying badge on each flag was redesignated to a different troop. Since these new troops were not ready in time for the Sedgemoor campaign it is unlikely that the new standards were being used. As the number of companies in the Foot regiments remained fixed they do not seem to been affected. many of the colours and standards of the Guards contained the royal ciphers in their design and it was therefore necessary to change them when a new monarch came to the throne.

First Foot Guards (1684) Colours during the time of Charles II

The King's Standard: crimson taffeta with CC interfaced under a crown, both in gold.
The Colonel's: white taffeta, with a crimson cross and a gold crown.
The Lieutenant-Colonel's: as above but with the CR cypher under the crown.
The Major as above with a crimson pile wavy.
The Captains all carried white flags with crimson crosses. Their company number from I to XX was shown in black in the top left-hand corner. Each company had its own badge in gold under a crown with the exception of the First captain who had a lion standing on the crown. The badges were; II a rose; III a fleur de lys; IV a portcullis; V a white rose and golden sun; VI a thisde; VII a harp; VIII a dragon; IX a white greyhound with a collar and gold ring; X a golden sun; XI a white unicorn with golden hoofs, mane and horn; XII a white antelope, with a coronet around its neck in gold, with gold chains and horns; XIII a white hart with gold coronet and chains; XIV a white falcon in a golden fetterlock, XV a golden rose with a stalk; XVI a white swan wearing a gold coronet with chains; XVII a white falcon, crowned, holding a golden sceptre; XVIII a tree trunk with growing leaves in gold; XIX emssed sword and aceptre in gold (sword blade as steel); XX the royal oak in gold.

First Foot Guards (1685) for the Coronation of James II

The Royal Standard: crimson taffeta with a crown and JR interfaced in gold.
The Colonel's: a plain crimson flag.
Lieutenant-Colonel's: white with a cross of St. George and a golden crown.
Major's: as above with a crimson pile wavy coming from the top left-hand corner.

The first to the twentieth captain were as the Lt. Colonel but with a smaller crown and a royal cypher underneath, the number of crowns and cyphers on the cross increasing to match the number of the Captain.

Coldstream Guards (1684) at the time of Charles II

The Colonel's: a plain blue flag.
Lieutenant-Colonel's: blue, with a crimson dross os. SL George edged white.
Major's: as above, with a white pile wavy from the left hand corner.

The Captains: as above with their respective numerals in place of the pile.

Coldstream Guards (1685) at the Coronation of James II

The Colonel's:.a plain white flag.
Lieutenant-Colonel's: white with a crimson cross.
Major's: as above with a pile wavy, colour unknown.

The captains' colours, were white with crimson crosses and in the centre, a golden crown with the captain's Roman numeral in white underneath from I to IX.

Life Guard (1684) at the time of Charles II

The King's and the Queen's troops carried crimson standards decorated by a crown and the royal cypher. The Duke of York's troop carried standards of yellow damask with a crown and the Duke's cypher.

The Horse Grenadiers attached to each troop carried guidons which differed from the standards only in that they had rounded and split ends.

Life Guard (1685) for the Coronation of James II

The King's troop had a standard of crimson damask, fringed with mixed gold and silver, three inches deep. The design was the king's cypher, topped by a golden crown with a silver scroll below carrying the motto Dieu et mon droit in black silk. Three small crowns were embroidered under the scroll. The guidon was as the standard but with a forked tail.

The second troop had a standard of white damask, fringed as above. Ile crown of gold was supported by two silver angels. 'The year of our Lord 1685' was wrought in gold under the cypher and the scroll was this time of gold but with the same. motto. The guidon was again the same but with a forked tail.

The third troop had a yellow damask standard but was in every other respect like that of the King's troop. The guidon again had a forked tail but was otherwise as the standard.

Oxford's Horse (Royal Regiment of Horse)

All the standards were of crimson damask with gold and crimson fringes. The various troops were distinguished by badges which had been granted by Charles II in 1661. In 1684 these were as follows: the king's troop, a crown;
the Colonel's, the royal cypher,, the majoes, gold streams; first troop, a rose crowned; second, a thistle crowned; third, a fieur de lys crowned; fourth, a harp crowned; fifth, the royal oak.

By 1685 further troops had been added to the regiment and the badges had been rearranged between the troops and further designs incorporated. The King's troop had the JR cypher and crown, above this in a silver scroll with the royal motto, and below all this, three small crowns. The Colonel had a lion mounted on a crown; the Lt.Colonel a golden rose crowned. The other troops had the following badges under a crown: a golden thistle; a fleur de lys; a golden harp with silver strings; a golden oak tree; a gold portcullis; the badge of the garter (red cross within blue ribbon).

Churchill's Dragoons (The Royal Dragoons)

The regiment carried crimson guidons, fringed with-crimson and silver. The troops were distinguished by a badge under a crown.

In 1684 the badges were: Colonel, the royal cypher (CC interlaced); Lt. Colonel, the rays of the sun issuing from a cloud; first troop, a beacon with flames; second, two ostrich feathers; third, a half rose half pomegranate with green leaves and stalk; fourth, a phoenix in flames.

By 1685 two extra troops had been added and the badges rearranged. The Colonel's as before retaining Charles II's cypher, Lt. Colonel, a gold escarbuncle (a kind of star, the badge of Henry VII); first troop, the ostrich feathers; second, the rose and pomegranate; third, the suns rays and cloud; fourth, the beacon; fifth, a tiger (?) with black, red and yellow spots, and flames coming from its, mouth; sixth, the phoenix.

Kirke's Foot (Queen Dowager's) (2nd Foot)

The Colonel's colour was sea green with two golden Cs interlaced (Catherine of Braganza's cypher) under a crown.
The Lt. Colonel's colour was sea green with a cross of St. George bordered in white, fine gold rays issued out to the corners of. the flag. The CC cypher and crown were in the centre.
The Major's was similar with a white pile wavy issuing from the top left-hand corner.
The remaining companies had designs similar to that of the Lt. Colonel's but with a Roman numeral over the crown.

Trelawney's Foot (Queen's, Majesty's or Queen Consort's) (4th Foot)

The Colonel's colour was white with the Queen's cypher MEBR in gold under a crown.,
The Lt. Colonel's was white with a SL George's cross with five eagles with golden beaks and legs in each quarter.
The major's was the same with a red pile wavy.
The first Captain's was as the Lt Colonells but with the Queen's cypher and crown in the centre.

It is not known if numerals distinguished the other companies, but this seems likely given the system in use with other regiments.

Earl of Dunbarton's Foot (Royal Regiment) (Royal Scots)

The Colonel's colour was plain white with a thistle in the centre under a crown surrounded by the motto Nemso me impune lacessit.
The Lt. Colonel's was blue with a St. Andrews cross and the same device.
The major's was the same but with a red pile wavy.
The Captain's colour was as the Lt. Colonel's distinguished by Roman numerals over the device.

Monmouth's Personal Standard

This is said to have been green with golden fringes and the motto 'Fear Nothing but God'.

A flag which may have been carried by Monmouth's army.

This flag is preserved in the National Amy Museum in London, where it is described as belonging to the period of the English Civil war. The canton contains the cross of St. George; the field is blue and the piles wavy are white. It remained in the hands of the same family for two hundred years, and tradition has it that it was carried by one of Monmouth's regiments. This cannot be confirmed but the flag is atypical of those of the Civil war, in that the different columns are separate pieces of material sewn on rather than painted on. We know that the schoolgirls of Taunton presented Monmouth with 27 flags and that one bore the cypher JR and a crown. After Sedgemoor, 22 rebel colours were captured, but there is no note of their appearance. We also know that the Somerset militia abandoned teir colours at Axeminster and these could have retained the Civil War system of denoting the company by the number of devices shown on the flag. It can be speculated that this flag was taken from the militia and used by the rebels.

Related

Sedgemoor Flag Illustrations (slow: 166K)