The subject line of the mail sent out by the two students of the high-performing Washington Latin Public Charter School said 'Bomb' and the email appeared to come from a Muslim student's account.
The message was in fact written by two pranksters, school officials were quoted as saying by the Washington Post.
The two boys, both high school seniors at school, were expelled for threatening violence, Head of School Martha Cutts was quoted as saying.
The email was sent Wednesday, and it was short, "Friday there will be big boom."
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The incident at Washington Latin was a case not of hacking but of opportunistic identity fraud, Cutts said.
A pair of students opened a laptop during class time and discovered that a previous user -- a student who happened to be Muslim -- had failed to sign out of his school email account.
School administrators quickly were able to figure out which laptop had sent the message and where that laptop was located when the email was sent. Armed with that information, it was not difficult to figure out who was to blame.
Muslim student is fine, Cutts said, and received a lot of support from other students.
Ibrahim Hooper, spokesman for the Council on American- Islamic Relations, said CAIR has seen an increase in bullying of Muslim students in recent years. He said the email should be considered anti-Muslim bullying and a hate crime.
In December, an emailed threat of violence prompted Los Angeles Unified -- the nation's second-largest school district -- to take the unprecedented step of shuttering schools for all 650,000 of its students.