- The Shadow over Innsmouth is a story of horror author H. P. Lovecraft, describing the investigation of the city of Innsmouth and the author's descent into madness. The set title is clearly inspired by the story.
- The double-faced card Aberrant Researcher transforms into a Insect Horror and thus mirrors the story of The Fly.
- The Thing in the Ice mirrors The Thing, a 1982 American science fiction horror film directed by John Carpenter. The movie was based upon the short story Who Goes There? by John W. Campbell, Jr., which in turn was inspired by Lovecraft's novella At the Mountains of Madness, in which an Antarctic research team uncovers a cryogenically preserved Elder Thing, which thaws out and attacks them.
- The flavor text of Rancid Rats references the H. P. Lovecraft story The Rats in the Walls.
- Accursed Witch is a play on the trope that killing a witch is dangerous because in their death they can curse their killer.
- Elusive Tormentor references vampires that can turn themselves into a mist.
- Just the Wind, It's Probably Nothing.
- Sleep Paralysis references the Night hag.
- Triskaidekaphobia is fear of the number 13.
- Brain in a Jar bears a strong resemblance to Gleemax.
- Relentless Dead and Shard of Broken Glass both depict the shattered remains of the stained glass windows of Thraben Cathedral, as depicted in Endless Ranks of the Dead.
- Lunarch Inquisitors were inspired by the Ghostbusters movie. When the Ghostbusters were out of the picture, the ghost would come back.
- The art of The Gitrog Monster bears a strong resemblance to Chub Toad.
- There are six different versions of Tamiyo's Journal, each with a different entry number in the flavor text corresponding to one of the six Clue tokens in the puzzle. How this affects card distribution in booster packs is unknown.
- Mark Rosewater (March 28, 2016). "Dark Shadows, Part 1". magicthegathering.com. Wizards of the Coast.
- gryffinp comments on “SOI Puzzle Clue token flavor texts”