The --databases option of the mysqlbackup command lets 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.) You can specify a space-separated list of database names, with the entire list enclosed in double quotation marks, or the absolute path (starting with a /) of a file containing the list of names, one per line.

Some or all of the database names can be qualified with table names, to only back up selected 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sure to include the same set of databases for every backup (especially incremental backups), so that you do not restore out-of-date versions of any databases.