Cain was the firstborn of Adam and Eve, both human hybrids of the First Civilization. At one point in his life, Cain killed his younger brother, Abel, in order to steal the Apple of Eden in his possession. Cain's mark, which he was given for killing Abel, eventually became the symbol of the Templars, a cross under which they united to collect more Pieces of Eden.
Clay Kaczmarek spoke of Cain in one of the Glyphs that he hid within the Animus data. He mentioned Cain's murder of Abel through quotes from the "Pearl of Great Price" scripture of the Church of Jesus Christ of Latter Day Saints.
- The Morse code message in Cain's Glyph translated to "Templar texts adapted by Mr. Smith". This likely alludes to Joseph Smith, the 19th century preacher who founded the LDS Church.
- The Templar pirate, Jing Lang mentioned the story of Cain and Abel while talking to Vance Travers about the assassination of his brother, Upton Travers.