You can make multiple calls to mysql_connect(), but if the parameters are the same you need to pass true for the '$new_link' (fourth) parameter, otherwise the same connection is reused.
so then you have
$dbh1 = mysql_connect($hostname, $username, $password);
$dbh2 = mysql_connect($hostname, $username, $password, true);
mysql_select_db('database1', $dbh1);
mysql_select_db('database2', $dbh2);
Then to query database 1, do
mysql_query('select * from tablename', $dbh1);
and for database 2
mysql_query('select * from tablename', $dbh2);
Alternatively, if the mysql user has access to both databases and they are on the same host (i.e. both DBs are accessible from the same MySQL connection) you could:
Example :
$migglecon = mysql_connect("localhost","root","123");
mysql_select_db("thefarmyard",$migglecon)or die(mysql_error());
$drupalcon= mysql_connect($localhost,$root,$123,true);
mysql_select_db("miggle",$drupalcon)or die(mysql_error());
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