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As of MySQL Version 3.23.6, you can choose between three basic table formats: ISAM, HEAP, and MyISAM. Newer MySQL may support additional table types (InnoDB, or BDB), depending on how you compile it.
When you create a new table, you can tell MySQL which table type it should use for the table. MySQL will always create a .frm file to hold the table and column definitions. Depending on the table type, the index and data will be stored in other files.