select a.id,a.item from table1 a, table2 b where a.item not in (b.entry);

explain
+----+-------------+-------+-------+---------------+---------+---------+------+--------+---------------------------------------------+
| id | select_type | table | type  | possible_keys | key     | key_len | ref  | rows   | Extra                                       |
+----+-------------+-------+-------+---------------+---------+---------+------+--------+---------------------------------------------+
|  1 | SIMPLE      | b     | index | NULL          | PRIMARY | 4       | NULL |  23916 | Using index                                 |
|  1 | SIMPLE      | a     | index | NULL          | PRIMARY | 6       | NULL | 265195 | Using where; Using index; Using join buffer |
+----+-------------+-------+-------+---------------+---------+---------+------+--------+---------------------------------------------+

select id,item from table1 where item not in (select entry from table2);

explain
+----+--------------------+------------------------+-----------------+---------------+---------+---------+------+--------+--------------------------+
| id | select_type        | table                  | type            | possible_keys | key     | key_len | ref  | rows   | Extra                    |
+----+--------------------+------------------------+-----------------+---------------+---------+---------+------+--------+--------------------------+
|  1 | PRIMARY            | table1                 | index           | NULL          | PRIMARY | 6       | NULL | 265195 | Using where; Using index |
|  2 | DEPENDENT SUBQUERY | table2                 | unique_subquery | PRIMARY       | PRIMARY | 4       | func |      1 | Using index; Using where |
+----+--------------------+------------------------+-----------------+---------------+---------+---------+------+--------+--------------------------+