The series started in 1995 when Jupiter Corporation developed Mario's Picross for the Game Boy.

Due to the popularity of pen-and-paper nonogram puzzles at the time in Japan, Makoto Nakayama, founder of Jupiter Corporation, pitched a video game version of nonograms to Nintendo.

Shigeru Miyamoto oversaw the process from Nintendo's side and proposed adding Mario to the game.

Shortly thereafter, HAL Laboratory, known for the Kirby series, developed Picross 3D for the Nintendo DS.

The game used similar mechanics to traditional Picross but adapted them to a three-dimensional environment.