Everything is fine, just one mistake is there. Change this:
$query = mysql_query("SELECT username FROM Users WHERE username=$username", $con);
$query = mysql_query("SELECT Count(*) FROM Users WHERE username=$username, $con");
if (mysql_num_rows($query) != 0)
{
echo "Username already exists";
}
else
{
...
}
SELECT *
will not work, use with SELECT COUNT(*)
.