The real Stanislav "Stas" Orlovski (George Tchortov), disguised as a waiter, hides a suppressed Beretta 92FS under table napkins in his mission to assassinate an anti-Russian government dissident named Victor Petrov in the pilot episode. Servicio Bolivariano de Inteligencia (SEBIN) agents use suppressed 92FS' when attempting to kill CIA agent Lopez. A renegade Mossad officer in a four-man team in Zurich, Switzerland is armed with the 92FS. Sudanese arms dealer and ex-CIA asset Hasaan Waleed (Conrad Coates) double taps a cargo ship captain with it when he is told of a higher fee to ship him and his crew to American soil. Jai (Sendhil Ramamurthy) seemingly preps a 92FS with a silencer when he thought that Ben Mercer went rogue again.
In "Bang and Blame" (S02E03), Roy Gaskin (Tim Guinee) and Annie Walker (Piper Perabo) are seen with the Beretta 92FS during shooting practice in the woods.
In "All the Right Friends" (S02E04), Jorge (Benito Martinez) is seen firing a Beretta 92FS at a hitman.
Beretta 92FS Inox
A Russian mobster in Communication Breakdown attempts to use an Inox model. Armed men with the regular 92FS and the Inox tried to kill Annie and Sophie Jacklin to cover up any loose ends regarding the "painting" that Russ Hilburn acquired.
Beretta M9A1
In "A Girl Like You" (S02E13), the bad guys are seen wielding silenced Beretta M9A1 which are fitted with green laser sights.
CZ 75B
In "The Outsiders" (S02E06), Jai (Sendhil Ramamurthy) and members of his team are seen with carrying CZ 75Bs.
Glock 17
A renegade Mossad hit team is seen using Glock 17's, both with and without suppressors. Ben Mercer (Eion Bailey) held a Glock 17 on Jai while trying to escape after forcing the CIA SOG team into a firefight with Waleed's men. A CIA guard (wearing white) aims his Glock 17 at Ben Mercer when he tries to approach CIA headquarters. One of the professor's kidnappers in Sri Lanka fire the Glock 17 at a retreating Ben before Jai fires his silenced pistol to kill him.
In "Horse to Water" (S02E14), Annie Walker (Piper Perabo) is shown firing a Glock 17.
Glock 19
In "Begin the Begin" (S02E01) an FSB agent is seen firing a silenced Glock 19 at Annie.
Glock 26
In "All the Right Friends" (S02E04), a hitman is seen with a silenced Glock 26.
SIG-Sauer P228
SEBIN agent Victor Ponces (Julian Acosta) uses a SIG-Sauer P228 for his sidearm, trying to shoot Annie in Venezuela when he was able to deduce her CIA identity. Annie uses the vehicle in disarming him by choking Ponces with the seat belt before she used her elbow. Agent Hughes (Paul Essiembre) also uses one to kill both Ponces and one of his agents.
SIG-Sauer P239
Mossad Officer Eyal Lavine (Oded Fehr) uses a SIG-Sauer P239 to defend Annie and himself after being ambushed by a renegade Mossad team. The half-height rear cocking serrations indicate that it's a 9mm.
In "Bang and Blame" (S02E03), a trainee is seen firing the Chiappa Rhino in the training exercise.
S&W Model 66
A henchman working under Hilburn is armed with a Smith & Wesson Model 66 with a 3" Barrel, supposedly to execute Annie until he was caught and disarmed by Jai and the police.
Unknown Revolver
Annie knocked it out from the hands of a bald Asian henchman who had kidnapped the professor in the finale of season 1.
Sub-Machine Guns
Heckler & Koch MP5K
In "Begin the Begin" (S02E01) assassins that come to kill Ben and Annie are both using Heckler & Koch MP5Ks.
In "A Girl Like You" (S02E13) Annie and Eyal come under attack and one of the attackers is seen with a Heckler & Koch MP5K.
Heckler & Koch MP7
In "Half a World Away" (S02E07), Auggie Anderson (Christopher Gorham) is seen with the Heckler & Koch MP7 during flashbacks to when he served in Afghanistan.
Rifles
AKMS
Hasaan Waleed's henchmen are seemingly armed with AKMS assault rifles.
In "Half a World Away" (S02E07), Auggie's Afghan escort and taliban terrorists are seen with AKMS rifles.
Colt Model 933
CIA guards are armed with the Colt Model 933 in the pilot episode.
M4A1
Used by the actual FSB assassin Stas in finishing off the false Stas in Washington D.C. in order to cover his tracks. Ben Mercer also uses a customized M4A1 assault rifle, outfitted with a suppressor and a scope to act as a short-range sniper rifle when he initiated a firefight between the SOG teams and Hasaan's henchmen. CIA guards in tactical gear aim their M4A1s at Ben Mercers outfitted with EOTech sights.
SIG 552
Used as the main assault rifle by a CIA SOG team in tactical gear after they were inserted by SUVs into the Brooklyn Shipyard to take Hasaan into custody instead of allowing the FBI's HRT to capture him due to political complications. All of them had suppressors.
Unknown AK-47
In "The Outsiders" (S02E06), Belarusian members of the Soviet Secret Police are seen with an unknown AK-47 variant.
Unknown M16/AR-15
In "Bang and Blame" (S02E03), a CIA Trainee is seen with an unknown M16/AR-15.
In "Half a World Away" (S02E07), members of Auggie's unit are seen with the same unknown M16/AR-15.
Shotguns
12 Gauge Double Barreled Shotgun
Ex-CIA agent Christopher McAuley (Eriq La Salle) is armed with a shotgun when he confronts Annie outside his cabin.
Ithaca 37 "Stakeout"n
An attacker is seen wielding an Ithaca 37 "Stakeout" in "A Girl Like You" (S02E13).
The FIM-92A Stinger is seen in weapon crates captured by law enforcement, noted to be from American military arsenals when shipped off to Hasaan in the 20th century before he went rogue.
Other
CAA Tactical RONI-G1
Members of the CIA Special Operations Group (SOG), are seen using Glock 17's mounted inside CAA Tactical RONI-G1's.
X26 Taser
In "Begin the Begin" (S02E01), a security guard is seen with a X26 Taser.
In "A Girl Like You" (S02E13) Annie Walker (Piper Perabo) finds an X26 Taser in the bag of foreign agent Eyal Lavine (Oded Fehr).
Extra
Sadiq's Stash Box
CIA Agent Jai Wilcox (Sendhil Ramamurthy) uncovered a storage space for a number of pistols after removing the false wall panel in the backroom of a Sudanese restaurant run by Sadiq an associate of Hasaan Waleed.