(covers information from several alternate timelines)
Antimatter missiles were a type of antimatter weapon.
In 2259 in the alternate reality, fired antimatter missiles were able to interfere with the threat assessment system aboard Starfleet Takayama-type shuttlecraft. A warning to this effect was noted on the pilot console. (Star Trek Into Darkness; )
In 2378, Ensign Harry Kim and Commander Chakotay discovered an antimatter missile while on the planet attempting to locate an old Earth deep space probe called Friendship 1, which had landed on the planet. The natives had developed antimatter missiles after gleaning information on antimatter-based technology from Friendship 1. The missiles remained stored in numerous underground missile silos even years after a power grid accident that triggered a nuclear winter on their homeworld.