The reason is because one of them does not have the privilege to view them all. I was having a issue with seeing all my tables in the mysql console and this is what fixed it. I had to log in as the root. (I'm using a linux computer)
$ /opt/lampp/bin/mysql -u
If its the other way around which phpmyadmin doesn't show all the databases is because you have put the wrong user in phpmyadmin source code. Change phpmyadmin settings to fix this.
tags:
phpmyadmin database does not match console
mysql hidden tables console
not all databases are shown in console
show all databases
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