Keanu Reeves turned down the role of Martin Brundle.
Chris Walas wanted Geena Davis to reprise her role as Veronica Quaife for the birth scene at the beginning of the film. Geena Davis declined, because she had found the maggot-baby dream sequence in the original film emotionally upsetting and was replaced by Saffron Henderson.
The first videotape of Seth Brundle (Jeff Goldblum) (where he theorizes that the teleporter improved him) is actually part of a deleted scene from The Fly (1986). The scene was slightly edited for this film, and Veronica's (Geena Davis) voice was dubbed over by Saffron Henderson (who plays Veronica at the beginning of The Fly II (1989)).
The Telepod props from The Fly (1986) were destroyed after filming was completed and had to be rebuilt.
John Getz (as Stathis Borans) is the only actor reprising a role from the original The Fly (1986).
The green flashes of light between each credit in the title sequence were actually borrowed from an alternate, unused title sequence for The Fly (1986).
In at least one draft of the script, Martin was going to see yet another videotape of Seth Brundle (this time nearing the end of his transformation), in which Seth talks about his "cure". This would have required brand-new footage of Jeff Goldblum in makeup from the previous film, and the concept was subsequently dropped from the script.
Geena Davis was offered the opportunity to appear in the film, but turned it down since Veronica Quaife was to be killed off very early on in the script, and had no real character development.
In some US states, theaters playing The Fly II (1989) had a nurse on hand for the audience's reactions to its content.
The movie was originally given an X rating by the MPAA because of the graphic scene where Hargis' head is crushed underneath an elevator. Director Chris Walas appealed the decision, and the MPAA gave the film an R rating without any edits to the scene.
The mutated Bartok monster was played by Mark Walas, brother of director Chris Walas.
David Cronenberg disliked the film.
An unusual trailer was made for the film that consisted of no footage, just an audio clip and the readout of a heart monitor with a woman, presumably Veronica Quaife, screaming about an unseen, painful birth.
An alternate ending had been filmed but deleted which Beth joins Martin outside the boathouse with a plate of food and sits next to Martin and asks how he feels, which he replies he is feeling a lot of better and a fly lands on the plate of food.
The role of Martin Brundle was written for Eric Stoltz to play. He originally declined the role because he didn't like the script. When the script was rewritten, he accepted the part.
Mel Brooks suggested to Chris Walas that Daphne Zuniga play Beth Logan, after Zuniga starred as Princess Vespa in Brook's "Star Wars" spoof Spaceballs (1987).
The book next to the sleeping technician in the control room at the beginning of the film is "The Shape of Rage", an anthology of writings about the films of David Cronenberg, who directed this film's predecessor.
Josh Brolin auditioned for the role of Martin Brundle.
Vincent D'Onofrio was the first choice for the role of Martin Brundle and was nearly cast for the part but his screen tests didn't go well. He was born the same year that Return of the Fly (1959) was released and he has the same first name as Vincent Price who appeared in The Fly (1958). He ended up playing a villainous bug named Edgar in Men In Black (1997).
When young Martin is shown playing with Dr. Shepard he's shown pulling on his tie, foreshadowing his death at the end when Martin becomes "Martinfly" and kills Shepard by strangling him by his tie.
In the 20th Century Fox intro, the sound of flies buzzing can be heard.
Originally, the film was going to be about cloning technology and Seth Brundle's resurrection. However, it was rejected.
A scene was taken out of the film which reveals the real reason why Bartok and his scientists can't get the Telepods to work and that the Telepods don't work because Stathis took the disc from the Telepods and all the research on it.
The Fly II (1989) was originally going to be filmed in Toronto, where The Fly (1986) was filmed, but they had no stage big enough for the sets and the only set big enough was Bridge Studios in Vancouver.
When Martin breaks into the security office and finds the video recording of Beth and himself having sex. He discovers footage of Seth Brundle telling Veronica Quaife about his disfigurement, caused by a fly being trapped inside the Telepod with him, which they were fused together. In that scene in the original film, it was not recorded on videotape.
Chris Walas turned down the offer to provide the special effects and puppet work on Gremlins 2: The New Batch (1990) to direct this film.
Saffron Henderson was chosen to play Veronica Quaife at the beginning of the movie due to her resemblance to Geena Davis.
Like Return of the Fly (1959), The Fly II (1989) was given a happy ending.
Eric Stoltz very much got into character and wanted to be called by his character's name and and had his character's name written on the back of his chair.
Garry Chalk (Scorby) was a comedian and people who knew him were concerned about his playing a serious role.
Although "The Fly III" never happened: A comic book sequel "The Fly: Outbreak" written by Brandon Seifert was published in 2015. "The Fly: Outbreak" takes place years after The Fly II (1989) and it follows Martin Brundle, as he attempts to cure Anton Bartok of his mutant condition.
20th Century Fox's decision to make Anton Bartok the film's antagonist was influenced by Alien (1979) and its sequel Aliens (1986), in which the evil Weyland-Yutani company is the real villain. Anton Bartok and his company Bartok Industries supplied Seth Brundle with the parts which Brundle used to construct the Telepods.
Daphne Zuniga said she took the role of Beth Logan because she was attracted to the character's strength and her emotional commitment to her relationship with Martin Brundle.
When she was interviewed about the film, Daphne Zuniga said that Beth Logan gets stronger by what happens in the movie and changes by the end of the movie. Beth's character arc is similar to Sarah Connor's in The Terminator (1984). Linda Hamilton, who played Sarah Connor, was David Cronenberg's first choice to play Veronica Quaife in The Fly (1986), but Geena Davis was cast.
David Cronenberg was not available to direct The Fly II (1989).
In the film, Martin Brundle due to his inherited mutant genes ages a lot faster, which in appearance he is 20 years old, underneath he is a 5 year old boy. In real life, there is a rare genetic disorder called Werner Syndrome, which is unusual accelerated aging (progeria).
Stuart Cornfeld, the producer of The Fly (1986), didn't not return to produce the sequel, due to a commitment on another production and Steven-Charles Jaffe took over as producer, after receiving a phone-call from Cornfeld, asking if he would be interested in producing the sequel and Jaffe agreed, after being asked if he liked The Fly (1986) and said he loved it.
There was a deleted scene of young martin coming across a freezer full of failed animal experiments like the dog that were teleported but was cut for pacing issues.
On a couple of occasions "Scorby" (Garry Chalk) addresses "Martin Brundle" (Eric Stoltz) as "Marty". Stoltz had started filming Back to the Future (1985) as Marty McFly before being replaced by Michael J. Fox. So Stoltz was first Marcty MC fly, then he was Marty THE fly.
John Getz agreed to return as Stathis Borans, but wanted to go somewhere with the character and came up with the idea of Stathis telling Martin not to sit in a chair.
Steven-Charles Jaffe and Chris Walas were unsure about Daphne Zuniga in the role of Beth Logan, because they had not seen any of her work. When the actress came in and read the part, Jaffe and Walas thought she was fantastic and she was cast.
Martin Brundle is born seven months after Vernoica Quaife killed Seth Brundle.
The sound effect of baby Martin crying in the opening scene was reused from Tin Toy (1988).
The word Beth types on the computer keyboard when Beth's cactus gets messed up in the Telepod demonstration is the word "fail".
The weapons Scorby and Bartok shoot Martin with are a Heckler & Koch HK9A3 and a Desert Eagle VII.
At 105 minutes, this is the longest Fly movie in the series.
Production designer Michael S. Bolton made a cameo in a scene that was filmed, but deleted. Beth stops at a snack bar on the way to Stathis's house. As Beth orders a burger and two big Pepsis, kids in a car parked next to Beth's car begin hassling Martin. Martin pops his head out and vomits on the car window frightening the children. Beth races back to the car. Martin's vomit has melted the car window. Beth gets in the car and drives way. The children's father comes out of the snack bar with burgers and Pepsis, which he angrily chucks on the ground when he sees Martin's vomit on the car.
Sam Raimi was the original choice to direct, due to the success of his horror flick Evil Dead II (1987). But, didn't get the job because it didn't work out due to Sam Raimi and his brother Ted Raimi writing a different treatment for the sequel which made it too wacky.
When Martin finds the videotape of Seth talking to Veronica about what being fused with the fly was a scene from the original movie and in the scene, it wasn't recorded on videotape by Veronica.
Although the film was given the 18 rating in the UK, the R rating in the US and the R16 rating in New Zealand. The film was given the M rating in Australia.
The people Martin kills in the film: His dog (albeit mercy kill), Dr. Jainway. Dr. Shepard. Mackenzie. Hargis and Scorby.
Baby Martin at the beginning of the film is played by Rodney Clough Jr..
The blue logo within the bartok name in the beginning of the film shares a close resemblance to the Minolta camera company logo.