Second generation Glock 17 pistols are used by the members of the FBI, most notably Charlie Francis (Kirk Acevedo). Francis demonstrates truly poor weapon handling at one point, positioning the thumb of his left hand on top of the slide. At the beginning of Season 1, Agent Dunham (Anna Torv)'s standard weapon is a Glock 17, with a Glock 26 as a BUG (as seen in episode 2). Midway through the season, she switches to the Glock 26 full-time.
A Glock 19 is Phillip Broyles (Lance Reddick) sidearm, although he rarely uses it. It is also seen very briefly in the hands of NYPD in one episode, and by Mitchell Lobe (Chance Kelley) before he is disarmed and taken into custody.
Olivia Dunham's (Anna Torv) sidearm is a sub-compact Glock 26, 9mm. The same sidearm is also used by Nick Lane, who was part of the same program as Dunham, likely prompting use of the same firearm. Agent Dunham's Glock 26 is borrowed once by Peter Bishop, who doesn't carry a gun himself.
A pair of .50AE Desert Eagles in chrome are requisitioned by Agent Dunham to kill the monster. Walter (John Noble) requests .50 caliber incendiary rounds in order to kill the creature, probably meaning a .50 caliber machine gun. Walter is surprisingly the one to kill the monster with two shots from his Desert Eagle. In the next shot, we can see that the gun has jammed after those two shots. A black Desert Eagle with a suppressor was also used by the assassin sent by the Observers in the episode "August" (S2Ep8).
Mitchell Lobe (Chance Kelley) uses a black, suppressed Kahr K9 9mm to execute the member of his bank robbery team who gets stuck in the vault; the Kahr is never seen with the slide forward, even when "fired." Mitchell's wife Samantha (Trini Alvarado) retrieves his Kahr K9 in stainless from a closet in order to try to kill Agent Dunham. Mitchell seems to have a thing for the K9.
The scientist who responds to the silent alarm at the genetics facility is armed with a Smith & Wesson Model 10. A S&W Model 10 HB is used by a store owner in S2Ep7.
A Beretta 92FS was used by a guard at a cryogenics facility in S2Ep4 where it is used to kill a shape shifter. In S2Ep7 a teenage mind controller makes Peter steal a Beretta 92FS from a policeman, then makes him shoot Agent Broyles with it.
Two of these are used by a shape shifter in S2Ep4 to kill the guards at a cryogenics facility. They appear to be Beretta Cougars. These are apparently standard equipment of guards for the mysterious antagonists in the show.
Error creating thumbnail: File missingBeretta Cougar - 9x19mm.Error creating thumbnail: File missingA guard fires his Beretta Cougars at the cryonics facility security. The standard team for "bad guy" operations seems to be a black guy with two pistols as security, a scientist type, and a generic white guy who gets shot first.Error creating thumbnail: File missingWhat looks like a pair of Beretta Cougars are dropped by the guard in the black van. S2Ep10.
Colt M1911A1
An old-looking Colt M1911A1 is used by a young woman under psychic possession by a Navy Officer. She retrieves it from his house.
The Sheriff of Edina and his Deputies carry Winchester Model 1912s in S2Ep12. They can be most easily identified by the large ejection port on the right side of the gun.
SWAT team members are seen with M4 Carbine rifles as they debark their van before storming a suspected biological laboratory. Soldiers equipped with NBC equipment also have M4 Carbines when they quarantine a building in "What Lies Beneath."
FBI SWAT officers can be seen armed with Heckler & Koch MP5A3's with Navy trigger groups, some of them also having Surefire dedicated forend weaponlights in the pilot and S2Ep7.
The Observer uses a pistol in S1E4 "The Arrival" to tranq Peter (Joshua Jackson). It looks a bit like a Walther PPK or a Detonics pocket 9 in S2E8 "August" the Observer pistol is shown to also fire sonic shock wave like the minority report Sonic Gun. it implied that is a advance weapons because Phillip Broyles said that the tech's can't get it to work.
Not seen clearly in an episode but seen in the special features for the episode where somebody teleports out of prison.
Unknown revolver
in the S2E20 "Brown Betty" private eye Dunham carries a revolver going with the 1940 Noir look of Walters story in the episode. It looked a bit like a Ruger GP100, although you only see it once, in a bad angle.
Battlestar Galactica sidearm
In the Season 2 Ep. 20 Brown Betty the Watcher hitmen (the Observers) carry what looks like the dressed up revolver used as the Colonial sidearm in the Battlestar Galactica mini-series.
Unknown pump-action shotguns
In Season 2 Ep. 21 Northwest Passage Peter buys a shotgun when he believes the shapeshifters are after him.
FN Five-seveN
The FN Five-seveN stands in as the futuristic sidearm of Fringe Division on the other side. It is referred to as the Model 76 handgun and was designed by William Bell. William Bell wields the 'Model 77' at one point which looks like it is merely another 5-7 with some different dressup components added to make it look different.
