Merge Two MySql databases

are they completely separate or they both contain the same tables?

might want to take a look at mysqldump and mysqlimport

Export one table, then import it in the other database....
If you are using PHPMyAdmin then follow the below:
OK. For example, database name: db1 and db2
The table name is tb.
Export table
1) Use phpMyAdmin, select db1
2) Click Export
3) Select db table
4) unselect Structure
5) check Save as file
6) Click Go

Import table
1) Use phpMyAdmin, select db2
2) Select db table
3) Click Import
4) Browse your exported file
6) Click Go

Done

they are contains same tables. I have tried to use export and import. But the problem is that there are fields for example article id. phpmyadmin gives duplicate id error.

then drop the table with same name.
or rename those tables and import them...

the problem is not the name of tables.
the problem is there are primary keys and also some tables connected with other tables
thus i could make import directly.

Download the trial of Navicat. If your tables have primary keys, you can compare or merge the two databases.

http://wiki.navicat.com/wiki/index.php/How_to_merge_two_tables_that_have_same_table_structure%3F

one option if you are dealing with duplicate id's is to create two tables in the same database, then create your queries to select into or update based upon a duplicate id