St. George was the patron saint of England, and the flag bearing his cross was the first "national" flag of England. During the reigns of Henry VIII and Elizabeth I, the Cross of St. George became the basic English naval flag. It also appeared as a canton in many of the striped ensigns of the latter's reign. These striped ensigns often featured green and white, the Tudor livery colors. When the monarch was present on board ship it was customary to fly the royal banner, and commanding admirals were sometimes permitted to fly it as a special mark of royal favor. The Tudor royal banner quartered the arms of France and England, reflecting the English monarch's claim to the French throne.

The earliest known version of the flag of the Lord High Admiral—a swallow-tailed crimson pennant bearing a golden anchor—dates from the reign of Henry VIII.
 

Royal Banner • Sixteenth Century

Cross of St. George • Ensign, Sixteenth Century Foremast Flag, 1606-34 • Jack, 1649

Blue and white ensigns were introduced in addition to the Red Ensign about 1625. Naval tactics were becoming more sophisticated at this time and the division of battle fleets into squadrons led to the introduction of distinctive squadron ensigns. This scheme survived, with variations, until 1864. Generally the Red Ensign was the senior color, but various changes were made over the years. In 1702, at a time when France was replacing the Dutch as England's principal naval rival, the White Ensign was modified by the addition of a broad Cross of St. George to distinguish it from the white ensigns of the French Navy. An ensign with horizontal red-white-red stripes and a small canton of the Cross of St. George was used briefly in 1702. As Lord High Admiral, James II flew a special ensign and masthead flag, both bearing the insignia of that office.

For each ensign there was a corresponding masthead pennant with the cross of St. George at the hoist. These pennants continued in use until the abolition of the three-ensign system in 1864, when the White Ensign and its corresponding pennant were prescribed for all commissioned ships of the Royal Navy.
 

Ensign of the Red Squadron • 1620-1707	Ensign of the Blue Squadron • 1620-1707
Ensign of the White Squadron  1630-1702 • 1702-07

The English Civil War, the execution of Charles I and the rule of Oliver Cromwell as Lord Protector resulted in several changes to British naval flags after 1649, but they all continued to be based on the established national symbols: the crosses of SS. George and Andrew. At first it was proposed to restore the Cross of St. George as the naval ensign of the Commonwealth, but the three existing ensigns were retained instead. New jacks adding a harp for Ireland were introduced, and there were several types of command flags for admirals. The Lord Protector's personal banner was also used as a naval command flag. The Union Flag, which symbolized the united crowns of England and Scotland, was dropped after the abolition of the monarchy, but it reappeared as a naval jack in 1658 with an escutcheon of the arms of Ireland. In 1659, a new ensign quartering the crosses of SS. George and Andrew was adopted.  But with the restoration of the monarchy in 1660, the Red, Blue and White ensigns, with the plain Union Flag, once more became the basic British naval flags.
 

Jack & Command Flag • 1649-58	Jack • 1658-60
Command Flag • Circa 1652	Lord Protector's Banner & Command Flag 1658-59

In 1707, new ensigns were established for the Royal Navy. All ships were ordered to fly the Union Flag as a jack and each squadron was given its own ensign displaying the First Union Flag in the canton. (In 1801 the diagonal red Cross of St. Patrick was added to the Union Flag.) These Red, Blue and White ensigns were used until 1864. In that year, the Union Jack and the White Ensign were reserved for the Royal Navy, the Blue Ensign was reserved for the use of qualified Royal Naval Reserve officers in command of merchant ships, and the Red Ensign became the British merchant ensign. All three are still in use today.

About 1700, the practice of using the royal banner as a command flag was abandoned. Thereafter, it was only flown at sea when the monarch was personally present. Queen Anne's royal banner displayed England impaled with Scotland in the first and fourth quarters, France in the second quarter, and Ireland in the third quarter. When the Elector George of Hanover assumed the British throne as King George I in 1714, the fourth quarter of the royal banner was altered to display his electoral arms.

Command flags for admirals of the three squadrons were white with the Cross of St. George, red and blue—hence the rank titles Vice-Admiral of the White, Rear-Admiral of the Red, etc. Exact rank was denoted by the mast from which the flag was flown: from the mizzenmast for a rear-admiral, from the foremast for a vice-admiral, and from the mainmast for an admiral. An Admiral of the Fleet (roughly equivalent to modern US five-star rank) flew the Union Jack at the main.

The Board of Ordnance was the government department responsible for the supply of weapons and munitions to the Army and Navy. Its vessels were permitted to fly a Red Ensign with the badge of the Board in the fly.

Some of the dates given with the drawings are approximate and it is likely that there were many deviations from the system described above. Commanding admirals, for example, often specified the flags to be flown by their fleets.
 

Royal Banner • Queen Anne • 1707-14

Royal Banner • House of Hanover • 1714-1801