Due to a poorly received test screening, David Ellison, a financier at Paramount, became concerned that the film was "too intellectual" and "too complicated," and demanded changes to make it appeal to a wider audience, including making Portman's character more sympathetic and changing the ending. Producer Scott Rudin sided with Garland in his desire to not alter the film, defending the film and refusing to take notes. Rudin had final cut.
Oscar Isaac filmed this movie and Star Wars: The Last Jedi (2017) on adjacent studio lots. He had the same trailer for both films and would often film scenes for both movies on the same day.
On December 7, 2017, it was announced that due to the clashes between producer Scott Rudin and David Ellison, a financier at Paramount, and the shift in Paramount's leadership, a deal was struck with Netflix handling international distribution rather than releasing the film in theaters. According to this deal, Paramount would handle the U.S. and China release, while Netflix would begin streaming the film in other territories seventeen days later.
Director Alex Garland decided not to reread the novel "Annihilation." Instead, he decided to adapt it "like a dream of the book."
Prior to its release, the film drew some criticism for the casting of Natalie Portman and Jennifer Jason Leigh as characters who are, in the books, described as Asian and half-Native American. Garland explained that none of the five female characters' ethnicity is revealed in the first book, which is the only one of the trilogy he has read, and that the script was actually complete before the second book was published. He cast the characters based on his reaction only to the actors he met in the casting process, or actors he had worked with before. Because he wanted to take the story in his own direction, he did not read the other two books while making the film in order to not be influenced by them.
Although the story is often said to be inspired by Tarkovsky's film Stalker (1979), in a Reddit AMA writer Jeff VanderMeer denied any inspiration from the film nor from the novel (Roadside Picnic) that it was based on.
The book Lena is reading during a scene with Kane is called "The Immortal Life of Henrietta Lacks," which is about an immortal cell known as HeLa, which was taken from Lack's cervical cancer cells in 1951.
Frances McDormand was considered for the role of Dr. Ventress before Jennifer Jason Leigh was cast.
The line that Ventress speaks in the tunnel where the meteorite struck ('Unfathomable mind. Now beacon. Now sea') is from Samuel Beckett's novel 'Molloy', itself the first part of a 'Trilogy', with 'Malone Dies' and 'The Unnamable'. In 'Molloy', the the title character is tracked down by a character called 'Moran'. Their identities appear to merge toward the end of the novel, which ties in with the theme of the double in 'Annihilation'.
Oscar Issac and Sonoya Mizuno previously starred together in Ex Machina (2014), which was also written and directed by Alex Garland.
This was the first R-rated film between Paramount Pictures and Skydance, and the second Skydance film overall to receive that rating.
Principal photography was underway by April 2016 when actor David Gyasi was added to the cast. Location filming by Lighthouse Pictures Ltd. occurred starting in late April in South Forest, Windsor Great Park. Some test shooting had already been done in St. Marks, Florida, but the vegetation in the area turned out to be too dense to give any perception of depth on screen. Lighthouse Pictures have a charge arrangement registered with U.K. Companies House regarding this matter. On May 9, 2016, cinematographer Rob Hardy began sharing pictures from the set of the film. On July 13 and 14, filming took place at Holkham Pines in North Norfolk. Shooting was completed that month.
In 2014, Paramount Pictures acquired rights to the novel with writer-director Alex Garland set to adapt the script and direct the film in May 2015. Natalie Portman soon entered into talks to star in the film. In November 2015, Jane the Virgin (2014) star Gina Rodriguez was in talks to co-star in the film with Portman and in March 2016, it was announced that Oscar Isaac would join the cast.
Both Oscar Isaac, the star of Alex Garland's previous movie, Ex Machina (2014), and Natalie Portman have starred in Star Wars movies. Isaac is in the Star Wars sequel trilogy and Portman was in the Star Wars prequel trilogy. Coincidentally, "Ventress" is also the name of a Star Wars Expanded Universe character.
Natalie Portman, Benedict Wong and Tessa Thompson have all starred in the Marvel Cinematic Universe. Portman played Jane Foster in Thor (2011) and Thor: The Dark World (2013), Benedict Wong played "Wong" in Doctor Strange (2016), and Thompson played Valkyrie in Thor: Ragnarok (2017).