The --databases and --databases-list-file options of the mysqlbackup command let you back up non-InnoDB tables only from selected databases, rather than across the entire MySQL instance. (To filter InnoDB tables, use the --include option instead.) With --databases, you specify a space-separated list of database names, with the entire list enclosed in double quotation marks. With --databases-list-file, you specify the path of a file containing the list of database names, one per line.

Some or all of the database names can be qualified with table names, to only back up selected non-InnoDB tables from those databases.

If you specify this option, make sure to include the same set of databases for every backup (especially incremental backups), so that you do not restore out-of-date versions of any databases.