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.
Director Alex Garland decided not to reread the novel "Annihilation." Instead, he decided to adapt it "like a dream of the book."
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.
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.
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.
The first base the crew encounters within the shimmer is named "The Southern Reach." The movie is based on the Southern Reach Trilogy.
Frances McDormand was considered for the role of Dr. Ventress before Jennifer Jason Leigh was cast.
Anya tells Lena when they first meet at the Southern Reach that "The people here put themselves to sleep in fetal positions." Earlier, when Lena wakes up for the first time at the Southern Reach after getting sedated, she is seen stirring from a fetal position.
During the lecture, Lena describes the cells in the video presentation as "cervical cancer" from a "31-year old patient." These are most likely HeLa cells, an immortalized cell line derived from a cervical cancer taken from Henrietta Lacks. The cells are widely used in Biomedical research, and the story of how cells from a patient biopsy were derived without her consent or knowledge is shown in The Immortal Life of Henrietta Lacks (2017). The movie is based on the book of the same name, and Lena is reading a copy of the book when she sits on the couch with Kane.
Natalie Portman had stated earlier in her career that she'd never be in a horror movie. She changed her mind to appear in Black Swan (2010) and this film as she really wanted to work with the filmmakers. Scheduling conflicts prevented her from appearing in Pride and Prejudice and Zombies (2016), which she auditioned for and won.
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.