The Los Angeles County district attorney's office has referred Aldon Smith's airport arrest earlier this month to the Los Angeles city attorney's office for misdemeanor consideration.
Smith was arrested at LAX for making a fake bomb threat.
The 49ers declined to comment on Thursday's development because the case is pending.
Smith, 24, has a court appearance Tuesday on felony gun charges and a drunken driving charge in Santa Clara (Calif.) County. He also faces potential discipline from the league.