The Disk Original Group (DOG) was a union formed of no less than seven Japanese video game companies: Square Co., Ltd., MicroCabin, Thinking Rabbit, Carry Lab, System Sacom, XTALSOFT, and HummingBirdSoft. Founded July 14, 1986, Square took the lead of this promising alliance to produce games on the Famicom Disk System. Because Square headed DOG, all DOG titles were published under the name Square. In reality, however, Square only produced a few of the eleven games published under the DOG label. In general, the games were commercial failures, leading to Square's brush with bankruptcy and the creation of Final Fantasy.

SquareSoft is a brand name used by Square between 1992 and 2003. As such, the name is often used (incorrectly) to refer to the entire organization, but its corporate name remained Square Co., Ltd. until the Enix merger.

Square Soft, Inc. was established as the official North American subsidiary of Square in March 1989. It was responsible for both the production and distribution of North American localizations of Square titles during the 16-bit era, and continued to produce English language localizations of Square games in the 32-bit era. It has also been responsible for localizing a number of non-Square titles, including Capcom's Breath of Fire for the SNES and Sony's Wild ARMs 3 for the PlayStation 2. It developed the game Secret of Evermore for the SNES. It is currently known as Square Enix, Inc. Square Soft's original headquarters were in Redmond, WA, where it distributed its now-dead newsletter, the Ogopogo Examiner, but it was relocated to Costa Mesa, CA in August 1996, where it remained until late 2005; as of 2006, Square Enix, Inc. is now located in El Segundo, California.

Square L.A., Inc. was established in August 1995. It was subsequently renamed Square USA, Inc.. It operates as a high-end computer-generated imagery research and development studio, and has been integral in the production of graphics for Square-produced games since the beginning of the 32-bit era. Its headquarters are in Los Angeles, CA and Honolulu, HI. Like its sister company, Square Soft, Inc., Square USA is a wholly owned subsidiary of Square Co., Ltd.

Square Electronic Arts, L.L.C. was a joint venture between Square and Electronic Arts (EA) established in May 1998 to distribute Square-produced game titles in North America. Its counterpart was Electronic Arts Square, K.K., in Japan, which was established to distribute EA games in Asia. Both companies were folded at the end of March 2003 as a result of the merger of Square and Enix.

Square Europe, Ltd. was established in December 1998 to localize and market Square-developed games in Europe and Australia. Located in London, England, Square Europe was granted exclusive publishing rights in Europe and other PAL territories for all interactive entertainment titles developed by Square.

DigiCube Co, Ltd. was established in February 1996. It was formed to market and distribute games and related merchandising (toys, books, music, etc.) in Asia. It declared bankruptcy in October 2003.

Square Pictures, Inc. was established in November 1997 to develop and produce computer-generated imagery films based on Square properties. It was folded in 2003, following the box-office failure of its only feature-length production, Final Fantasy: The Spirits Within. However, it did survive just long enough to create the CGI short-film, Final Flight of the Osiris for The Matrix spin-off DVD, Animatrix.

Quest was an independent software development studio established in July 1988, best known for the Ogre Battle series. Several team members, including Yasumi Matsuno, Hiroshi Minagawa and Akihiko Yoshida, left Quest in 1997 to join Square, where they worked on several titles for the Sony PlayStation, including Final Fantasy Tactics and Vagrant Story. In June 2002, Quest was purchased by Square.

Square Visual Works Co., Ltd. (CG Studio), Square Sounds Co., Ltd. (Sound Studio), Squartz Co., Ltd. (Quality Assurance) and Square Next Co., Ltd. were all founded in June 1999. All were subsequently absorbed into Square Co., Ltd. in 2001 and 2002.