The rose is an ancient symbol of secrecy, hence "sub rosa". From Wikipedia:
In Hellenistic and later Roman mythology, roses were associated with secrecy because Cupid gave a rose to Harpocrates (the Hellenistic silence god) so that he would not reveal the secrets of Venus. Banquet rooms were decorated with rose carvings, reportedly as a reminder that discussions in the rooms should be kept in confidence. This was inherited in later Christian symbolism, where roses were carved on confessionals to signify that the conversations would remain secret.
I only found that out this morning; it came up in a book I was reading on a secret society. I could tell you which one, but then I'd have to kill you.
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