MySql `DELETE` syntax is not very different fiom `SELECT`, so you can delete from multiple tables using a single query.

Taxonomies informations in WordPress are in 3 tables:

 - `wp_terms`
 - `wp_term_taxonomy`
 - `wp_term_relationships`

the first 2 contain term / taxonomy informations, the 3rd contains association between terms and posts.

The query to delete **all** tags from WordPress db is:

    DELETE t, tr, tt
    FROM wp_terms t  
    INNER JOIN wp_term_taxonomy tt ON t.term_id = tt.term_id
    INNER JOIN wp_term_relationships tr ON tt.term_taxonomy_id = tr.term_taxonomy_id
    WHERE tt.taxonomy = 'post_tag'

Note that the prefix `wp_` can be different in your setup, it depends on `$table_prefix` setting on your `wp_config.php` file. More info [here][1].

Be sure to replace the prefix with correct value in the query for all the 3 tables.

Also note that on [**multisite**][2] install, the full table name is

    $prefix . $blogid . '_' . $tablename`

e.g. if the prefix is the default `'wp_'` the blog is 2, the 3 tables will be named:

 - `wp_2_terms`
 - `wp_2_term_relationships`
 - `wp_2_term_taxonomy` 

More info [here][3].

Finally, please, **be sure to have a full, valid database backup before running such a query**.


  [1]: http://codex.wordpress.org/Editing_wp-config.php#table_prefix
  [2]: http://codex.wordpress.org/Create_A_Network
  [3]: http://codex.wordpress.org/Database_Description#Site_Specific_Tables