Mary Queen of Scots cipher

The Mary Queen of Scots cipher is a hybrid system that combines:

1. A homophonic substitution — several distinct symbols per plain letter, to flatten frequency distribution.
2. A nomenclator — a table of whole words or proper nouns coded by a single symbol (a built-in code dictionary).

It entered history because it was the cipher used by Mary Stuart, Queen of Scots, in her secret correspondence with Anthony Babington in 1586. The decryption of that correspondence provided the written evidence that Mary was plotting Elizabeth I’s assassination — evidence that sent her to the scaffold in February 1587.

Historical context

Mary Stuart, the deposed Queen of Scots, has been imprisoned in England since 1568 on Elizabeth I’s orders. Her correspondence is constantly surveilled by Secretary of State Sir Francis Walsingham, chief of the English Secret Service.

In 1586, Anthony Babington, a young English Catholic, contacts Mary through what he believes is a secret channel: letters slipped into the bung of beer barrels delivered to her prison. He proposes a plot: assassinate Elizabeth, free Mary, restore Catholicism in England.

Unbeknownst to them, Mary and Babington use a channel entirely controlled by Walsingham: the messenger (Gilbert Gifford) is a double agent, and every letter is intercepted, copied and decrypted before being passed on.

The cipher

Structure

The table contains:

• 23 homophonic symbols for the 23 Latin letters (no J, U, W).
• 35 special symbols for common words and phrases: “the”, “of”, “from”, “with”, names of sovereigns, salutation formulae.
• 5 “filler” symbols with no value, sprinkled at random to confuse cryptanalysis.

Sample table (reconstructed)

A → ƒ          B → ¥          C → §
D → α          E → £ or Δ     F → ω
G → ¢          H → #          I → 7
…
"the"   → ⊕   "of" → ⊗   "Babington" → ⌐

A typical Mary Stuart letter ciphertext looks like:

ƒ§7§ § ⊕ ¥α§ ⊗ § ƒ£# ⌐ # ƒ ¢ƒ #

— a visually intimidating mosaic, designed to discourage any lateral reading.

Phelippes’s cryptanalysis

Thomas Phelippes (1556–1625) is Walsingham’s personal cryptanalyst. A polyglot (English, French, Italian, Latin, Greek), he is one of the earliest specialists of frequency analysis enriched with cribs.

His method on the Mary Stuart cipher:

1. Salutation guess — every letter starts with a variation of “Right honourable” or a direct reference to Mary. That gives 10–15 initial symbols with probable values.
2. Filler identification — some symbols show no correlation with their neighbours; they are dismissed.
3. Homophone detection — by cumulative frequency, the 3–4 symbols matching the same plain letter become identifiable.
4. Nomenclator reading — clumps of unique symbols between regular letters encode words; they are deduced from context (“the”, “Queen”, “death”).

Phelippes broke the cipher in a few weeks.

The forgery that sealed her fate

Walsingham, having read the exchanges in plaintext, asks Phelippes for something extraordinary: forge a letter from Mary to push Babington into revealing his co-conspirators. Phelippes, now master of the cipher, drafts a fake letter in cipher that is perfectly credible, asking Babington for the list of plotters.

Babington replies — the list is intercepted, and arrests begin. Mary is tried for high treason at Fotheringhay (1586), sentenced to death, executed on 8 February 1587.

Cryptanalytic legacy

The Mary Stuart cipher marks:

• The rise of state cryptanalysis as a political weapon.
• The end of the illusion that homophonic + nomenclator is inherently safe.
• The appearance of ciphertext forgery as a psychological-operations technique.
• The need for authenticity in encrypted communication — Babington accepted the forged letter because no authentication mechanism existed.

It is also a lesson for modern cryptography: confidentiality without authenticity is not enough. Modern protocols (TLS, Signal) encrypt AND sign — Walsingham could no longer mount exactly the same attack today.