MERGE child tables are locked through the parent table. If the parent is a temporary table, it is not locked, and thus the child tables are also not locked; this means that parallel use of the underlying MyISAM tables corrupts them.

If you use ALTER TABLE to change a MERGE table to another storage engine, the mapping to the underlying tables is lost. Instead, the rows from the underlying MyISAM tables are copied into the altered table, which then uses the specified storage engine.

The INSERT_METHOD table option for a MERGE table indicates which underlying MyISAM table to use for inserts into the MERGE table. However, use of the AUTO_INCREMENT table option for that MyISAM table has no effect for inserts into the MERGE table until at least one row has been inserted directly into the MyISAM table.

A MERGE table cannot maintain uniqueness constraints over the entire table. When you perform an INSERT, the data goes into the first or last MyISAM table (as determined by the INSERT_METHOD option). MySQL ensures that unique key values remain unique within that MyISAM table, but not over all the underlying tables in the collection.

Because the MERGE engine cannot enforce uniqueness over the set of underlying tables, REPLACE does not work as expected. The two key facts are:

Similar considerations apply for INSERT ... ON DUPLICATE KEY UPDATE.

MERGE tables do not support partitioning. That is, you cannot partition a MERGE table, nor can any of a MERGE table's underlying MyISAM tables be partitioned.

You should not use ANALYZE TABLE, REPAIR TABLE, OPTIMIZE TABLE, ALTER TABLE, DROP TABLE, DELETE without a WHERE clause, or TRUNCATE TABLE on any of the tables that are mapped into an open MERGE table. If you do so, the MERGE table may still refer to the original table and yield unexpected results. To work around this problem, ensure that no MERGE tables remain open by issuing a FLUSH TABLES statement prior to performing any of the named operations.

The unexpected results include the possibility that the operation on the MERGE table reports table corruption. If this occurs after one of the named operations on the underlying MyISAM tables, the corruption message is spurious. To deal with this, issue a FLUSH TABLES statement after modifying the MyISAM tables.

DROP TABLE on a table that is in use by a MERGE table does not work on Windows because the MERGE storage engine's table mapping is hidden from the upper layer of MySQL. Windows does not permit open files to be deleted, so you first must flush all MERGE tables (with FLUSH TABLES) or drop the MERGE table before dropping the table.

The definition of the MyISAM tables and the MERGE table are checked when the tables are accessed (for example, as part of a SELECT or INSERT statement). The checks ensure that the definitions of the tables and the parent MERGE table definition match by comparing column order, types, sizes and associated indexes. If there is a difference between the tables, an error is returned and the statement fails. Because these checks take place when the tables are opened, any changes to the definition of a single table, including column changes, column ordering, and engine alterations cause the statement to fail.

The order of indexes in the MERGE table and its underlying tables should be the same. If you use ALTER TABLE to add a UNIQUE index to a table used in a MERGE table, and then use ALTER TABLE to add a nonunique index on the MERGE table, the index ordering is different for the tables if there was already a nonunique index in the underlying table. (This happens because ALTER TABLE puts UNIQUE indexes before nonunique indexes to facilitate rapid detection of duplicate keys.) Consequently, queries on tables with such indexes may return unexpected results.

If you encounter an error message similar to ERROR 1017 (HY000): Can't find file: 'tbl_name.MRG' (errno: 2), it generally indicates that some of the underlying tables do not use the MyISAM storage engine. Confirm that all of these tables are MyISAM.

The maximum number of rows in a MERGE table is 2⁶⁴ (~1.844E+19; the same as for a MyISAM table). It is not possible to merge multiple MyISAM tables into a single MERGE table that would have more than this number of rows.

Use of underlying MyISAM tables of differing row formats with a parent MERGE table is currently known to fail. See Bug #32364.

You cannot change the union list of a nontemporary MERGE table when LOCK TABLES is in effect. The following does not work:

CREATE TABLE m1 ... ENGINE=MRG_MYISAM ...;
LOCK TABLES t1 WRITE, t2 WRITE, m1 WRITE;
ALTER TABLE m1 ... UNION=(t1,t2) ...;

However, you can do this with a temporary MERGE table.

You cannot create a MERGE table with CREATE ... SELECT, neither as a temporary MERGE table, nor as a nontemporary MERGE table. For example:

CREATE TABLE m1 ... ENGINE=MRG_MYISAM ... SELECT ...;

Attempts to do this result in an error: tbl_name is not BASE TABLE.

In some cases, differing PACK_KEYS table option values among the MERGE and underlying tables cause unexpected results if the underlying tables contain CHAR or BINARY columns. As a workaround, use ALTER TABLE to ensure that all involved tables have the same PACK_KEYS value. (Bug #50646)