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The working title of the film was The Monster from Beneath the Sea. After the credits, voice-over narration introduces the team of scientists and their secret project, "Operation Experiment." According to an August 1953 Variety news item, producers Jack Dietz and Hal Chester originally offered their independent film, which they made for $285,000, to RKO, but the studio declined the offer, despite the success of the producer's 1933 production for RKO, King Kong. The article reported that Warner Bros., interested in entering the science fiction market, then paid $400,000 for the film. The studio budgeted an additional $250,000 for a radio and television ad campaign, which was described in an April 1953 Hollywood Reporter news item as a coast-to-coast campaign, preceding a 500-city multiple premiere.
According to a modern source, Warner Bros. also replaced the original score with an orchestral one by David Buttolph and added the scene at the ballet. The beast, which was called a "rhedosaurus" in the film, was designed and animated by Ray Harryhausen, using a low-budget stop-motion technique called "Dynamation." The Beast from 20,000 Fathoms was Harryhausen's first major film credit. Director Eugene Louri admitted, in an April 1953 Daily Variety news item, that the creature was completely imaginary, as they wanted to create a monster that was "more frightening than the real thing." According to a May 1953 Los Angeles Daily News article, eight men were needed to operate the beast.
The character of the surviving seaman portrayed by Jack Pennick, who was listed as "Jacob" in the New York Times and Variety reviews, was called "George LeMay" in the film. Portions of the film, according to a modern source, were shot in locations in New York City, including Wall Street and the Stock Exchange. Modern sources add George R. Grover and Max M. Hutchinson to the sound crew, Clarence Kolster as film editor, and stuntman Gil Perkins. The following actors were added to the cast by modern sources: Ed Clark (Lighthouse keeper), Franklyn Farnum (Ballet patron), Fred Aldrich (Radio operator), Joe Gray (Longshoreman) and Louise Colombet (Nun).
One modern source also states that Louri later claimed that he and an unnamed blacklisted writer contributed to the screenplay, which was signed by writers Lou Morheim and Robert Smith. Morheim and Fred Freiberger are credited onscreen with the screenplay. The source speculated that Smith was a pseudonym for the blacklisted writer. One of the plot points partially retained in the screenplay from Ray Bradbury's original short story was the lighthouse scene. However, in Bradbury's version, the beast is lured to the lighthouse by the sound of the foghorn, which it mistakes for a mating call. The short story was later retitled "The Foghorn" when published in Bradbury's anthology The Golden Apples of the Sun.