It stems from an Instagram post shared by Comey, which contained an image of seashells on a beach arranged to read "86 47". "Eighty-six" is a slang term for "get rid of", and prosecutors allege it encourages violence against Trump, the 47th president.
Comey denies any wrongdoing, saying he did not know what the numbers meant, and accused the prosecution of political motivation.
This marks the second time the justice department has brought criminal charges against Comey, a long-time critic of Trump.