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The Latin phrase sub rosa means "under the rose" and is used in English to denote secrecy or confidentiality, similar to the Chatham House Rule. The rose as a symbol of secrecy has an ancient history.
The rose has held a deeply symbolic significance in many times and cultures as a symbol of maternal creativity and of the yoni or feminine generative power.. The literal rose and its essence or attar has also played a role in religious and spiritual rites which ofttimes would have been held in secret.
The rose has sometimes been said to have been the emblem of the god Horus in ancient Egypt. However the gods in Egypt were usually associated with the lotus. The idea of Horus being linked to the rose probably arises from Greek and Roman cultural cross-transmission of myths from Egypt. Firstly, the rose's connotation of secrecy dates back also to Greek mythology. Aphrodite gave a rose to her son Eros, the god of love; he, in turn, gave it to Harpocrates, the god of silence and a Greek name for a form of Horus, to ensure that his mother's indiscretions (or those of the gods in general, in other accounts) were not disclosed. Secondly, in Egypt, the rose was actually sacred to Isis but this appears to have been during the Roman period of Egyptian history - "Probably due to assimilation with the goddess Aphrodite (Venus), during the Roman period, the rose was used in her worship." The demand for roses throughout the empire turned rose production into an important industry.
Later, the Greeks and Romans translated the god's Egyptian name Heru-pa-khered as Harpocrates and regarded him as the god of silence. The association of Harpocrates with silence and secrecy originates from a misunderstanding of Egyptian depictions of the god. Heru-pa-khered was represented as a naked youth with a finger-to-mouth gesture—in Egyptian artwork this gesture imitates the hieroglyph for child and is used to represent youth, but was misunderstood by later Greeks and Romans as a gesture for silence.
Paintings of roses on the ceilings of Roman banquet rooms were also a reminder that things said under the influence of wine (sub vino) should also remain sub rosa.
In Christian symbolism, the phrase "sub rosa" has a special place in confessions. Pictures of five-petalled roses were often carved on confessionals, indicating that the conversations would remain secret. The phrase has also been understood to make reference to the mysterious virginal conception of Christ.
The rose is also an esoteric symbol of Rosicrucianism which was often considered to be a secret society or brotherhood.
In the 16th century, the symbol of Henry VIII of England was the stylised Tudor dynasty rose. A large image of the rose covered the ceiling of the private chamber where decisions of state were made in secret.
Special Forces usage 
More recently, "sub rosa" activities have become a byword for covert operations, usually by security services. Originating primarily in the Canadian and American special forces, this meaning has been gradually spreading to other countries and in particular the United Kingdom. To refer to covert operations, the Special Boat Service uses the term in the vernacular.
J. Edgar Hoover 
At the time head of the FBI, he kept secret files on politicians, leading figures of society and gansters/organised crime. This mass of data was used to manipulate the people in power for his own means. This data got so detailed and extensive that he stored the files at his house in the basement. This basement extended out from the house under his beloved rose bushes. The files were the the start of the C.I.A. Which makes the C.I.A. sub-rosa.
Hungarian usage 
For many Hungarians, the expression "sub rosa" originates from the time of Wesselényi conspiracy in 1670. According to the legend, the conspirators organised their meetings in a secluded small balcony room in the Rákóczi castle at Sárospatak. In the middle of the painted ceiling there is a rose. While in reality it was probably just a pun, using both the literal "under the rose" meaning of "sub rosa" as well as its reference to secrecy, many Hungarians believe that the latter meaning of the expression originated from the conspiracy, which, in fact, is known as the "Sub-rosa conspiracy" in Hungary.