Prince Philip, later Philip II of Spain, was entrusted with regency when his father, Emperor Charles V, left Spain in May 1543, when he was about to turn sixteen.
A cipher used in the first year of Philip's regency can be reconstructed from an undeciphered letter of Suarez de Figueroa to Prince Philip of 20 November 1543 (PARES) by using the clear text of the letter of 17 November 1543 (PARES). This cipher may have been the first cipher in his correspondence (not that he did the (de)ciphering himself). I tentatively call it the Figueroa-Philip Cipher (1543).
(Philip II is known to have paid attention to information security by use of ciphers, but he was not versed in the practice himself. Geoffrey Parker (2014), Imprudent King: A New Life of Philip II reproduces the King's letter to the Duke of Alba of 7 August 1567 in his own hand and points out that he enciphered only key words instead of whole passages and enciphered a word letter by letter rather than using a symbol for combinations (Fig. 28).)
See another article to see this and other Spanish ciphers used at the time.
The following describes my initial attempt at codebreaking, with partial success, before I noticed a plaintext was available.
At first glance, I supposed from the use of superscript numerals that the basic structure would be the same as that of the Doria-Figueroa-Philip Cipher (1548) based on the vowel indicator system.
Word boundaries discernible here and there provide a promising clue. Moreover, "v. al." appeared to be in clear ("vuestra alteza"). So 4 occurring before "v. al." would be either A or DE.
It was noted the pattern δ'4gw4ρ34 (ciphertexts reproduced herein are not-so-close approximations) occurred several times. Assuming w4 and ρ3 both represent a syllable (vowel + consonant), I first assumed ρ3=RI and 4=A (which turned out to be correct). Words matching this pattern such as CALVARIA, SALVARIA, etc. were found in a dictionary but did not seem right.
The pattern ∞a'σ' was very frequent. I once thought of a possibility of a three-letter code symbol, but separate occurrences of a' and σ' assured that these were three cipher symbols. The most frequent trigram in Spanish is QUE, which is consistent with the fact that ∞ is always followed by a'. Then, the two-letter word σ'3 might be EN. (This later turned out to be ES forming only a part of a word. That is, the space between symbols does not always correspond to actual word boundaries.)
There are four-letter patterns beginning with QUA, which appeared to be QUAL and thus allowed identification of a symbol for L. Three-letter patterns ending in EL indicated DEL and thus identified a symbol for D.
I also assumed w2+L was DEL, which identified w2=DE.
A striking weakness of the vowel indicator system is that identification of one syllable reveals other syllables for the same consonant. Thus, w2=DE and ρ3=RI suggests w4=DO, which led to a hypothesis that the above-mentioned pattern δ'4gw4ρ34 might be ***DORIA, such as *AL DORIA. (In the end, this turned out to be "capitan JUAN DORIA".)
On the first line, "v. al." in clear is followed by U+L+p3. If the superscript 3 is I as in ρ3=RI, I thought this might be a Spanish counterpart for the English "ultimo."
On the third page, the letter seems to end with a date line and the margin has something like "Dupp." Although the remaining text cannot be a duplicate for the preceding portion from its shortness, I found several words at the beginning and the end matched those of the first portion. It allowed identification of some homophones: ω6=a'c. But this ended up in confusing me because I thought it contradicted the above finding that w2=DE. (I should have realized w, which has an overbar, and ω were different symbols.)
At this point, I checked other letters from Suarez of Figueroa to Prince Philip to see typical expressions used at the beginning or around "v. al." The following specimens were found.
From these specimens, I was almost certain that the beginning of the letter Θu73 was A-LO-S.
I might proceed like this to identify other symbols but I thought letters of closer date might provide more clues. As expected, the letter of 17 November had "a. vl. ultimamente" near the beginning. The word "ultimamente" was what I was looking for. As it turned out, this was not the only word corresponding to the ciphered letter. This letter of 17 November turned out to provide the plaintext of the cipher letter of 20 November.
The first half of the ciphertext of 20 November 1543 is generally identical with the clear text of 17 November 1543 but there are the following differences:
(i) the fourth line of the ciphertext lacks "y con esta va el duplicado" present in the clear text;
(ii) the fifth to third lines from the bottom of the second page of the ciphertext has something like "... de la gente que se va y a el sacadole los ojos como mas particularmente entende ? v.al. por los despachos que van con estadel Marques don Pe[d?]ro Goncalez de Mendoca a los quales me remito." The corresponding clear text (the last two lines on the second page) is much shorter and reads something like "... la gente gon? Clauaua con mos particularmente haura v. al. entendid? por la Cotra".
(iii) the clear text appended to the first half of the ciphertext is different from the ending remark of the clear text.
These differences might only concern different routes of the two copies.
The second half of the ciphertext, of which a counterpart is not present in the 17 November letter, begins with something like "Lo de hasta a que es copia de otra qui? escrivi a v. al. con una cara vela que despacho de a qui a Barcelona y agora parti una navidon de va el ordinario de ...." As with the first part, the clear text may be found somewhere in the archives.
S. Tomokiyo, Spanish Ciphers during the reign of Emperor Charles V
S. Tomokiyo, Spanish Ciphers during the Reign of Philip II