Bolton fell out badly with President Donald Trump since serving in his first term and has become a strident critic of the populist president.
The approval of charges by a federal grand jury in Maryland marked the latest legal moves by the administration against political adversaries.
The indictment, which draws upon investigations which gained pace under the presidency of Joe Biden, accuses Bolton of sending over a thousand pages of so-called diary notes about his duties in 2018 and 2019.
Bolton, prosecutors allege, used his AOL email account and an insecure messaging app to transmit some materials to two unnamed people who lacked security clearances.
Those messages, the indictment added, included “national defense information” including top secret classified material.
On or around July 6, 2021, the indictment alleged, a Bolton representative contacted the FBI, saying, "evidently someone has gotten into Amb. Bolton's personal email account and that it looks as though it is someone in Iran."