A cipher used in letters from Thomas Wilkes to Sir Francis Walsingham, Queen Elizabeth's spymaster, is given below. It is a simple pigpen cipher together with a nomenclature in numbers, letters, and pseudonyms for representing words and names.
Wilkes was sent in 1586 to the Dutch Republic to keep an eye on the Earl of Leicester, who accepted (25 January 1586) the title of Governor-General of the United Provinces struggling against the Spanish monarchy. His reports to Walsingham grew increasingly critical of Leicester (Wikipedia).
Wilkes' letters to Walsingham are available in Digital Collections of BYU Library. The cipher is used in the letters below. The above reconstruction is based on the letter of 26 March 1587, supplemented with others that use cipher only sparingly.
7 August 1586 (no cipher)
19 April 1587 (no cipher)
The above is a second instance of a pigpen cipher I know from the sixteenth century. The first is a pigpen cipher of Philip II's agent (1577) (see my blogpost).
Ciphertext in pigpen cipher in TNA SP106/10 is solved by Daniel Bourdeau. He dates the message in French to the seventeenth century.