MySQL uses a cost-based optimizer to determine the best way to resolve a query. In many cases, MySQL can calculate the best possible query plan, but sometimes MySQL doesn't have enough information about the data at hand and has to make “educated” guesses about the data.
For the cases when MySQL does not do the "right" thing, tools that you have available to help MySQL are:
Use the EXPLAIN statement to get information about how MySQL will process a query. To use it, just add the keyword EXPLAIN to the front of your SELECT statement:
mysql> EXPLAIN SELECT * FROM t1, t2 WHERE t1.i = t2.i;
EXPLAIN is discussed in more detail in EXPLAIN.
Use ANALYZE TABLE tbl_name to update the key distributions for the scanned table. See ANALYZE TABLE.
Use FORCE INDEX for the scanned table to tell MySQL that table scans are very expensive compared to using the given index. See SELECT.
SELECT * FROM t1, t2 FORCE INDEX (index_for_column) WHERE t1.col_name=t2.col_name;
USE INDEX and IGNORE INDEX may also be useful.
Global and table-level STRAIGHT_JOIN. See SELECT.
You can tune global or thread-specific system variables. For example, Start mysqld with the --max-seeks-for-key=1000 option or use SET max_seeks_for_key=1000 to tell the optimizer to assume that no key scan will cause more than 1,000 key seeks. See the section called “Server System Variables”.