The Isu created the Pieces of Eden in Assassin's Creed.
The Isu, also called the First Civilization, are an advanced precursor species that existed on Earth before modern humans. They created powerful artifacts, including Apples, Staves, and other Pieces of Eden. These objects could influence human minds, alter perception, or perform other extraordinary functions.
The Templars and Assassins seek, protect, or use Pieces of Eden across different historical periods, but neither faction created them. “The First Civilization” is a description or alternate name for the Isu rather than a separate group, which is why the most specific canonical answer is the Isu.
The games reveal Isu history through genetic memories, ruins, holographic messages, and recovered artifacts. Important Isu figures include Minerva, Juno, and Jupiter. Their earlier creation of humans and later catastrophe form a major part of the franchise's science-fiction mythology.