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.

REPLACE does not work.

You cannot use DROP TABLE, ALTER TABLE, DELETE without a WHERE clause, REPAIR TABLE, TRUNCATE TABLE, OPTIMIZE TABLE, or ANALYZE 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, which yields unexpected results. The easiest way to work around this deficiency is to ensure that no MERGE tables remain open by issuing a FLUSH TABLES statement prior to performing any of those operations.

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 allow 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.

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 (depending on the value of the INSERT_METHOD option). MySQL ensures that unique key values remain unique within that MyISAM table, but not across all the tables in the collection.

When you create a MERGE table, there is no check to ensure that the underlying tables exist and have identical structures. When the MERGE table is used, MySQL checks that the row length for all mapped tables is equal, but this is not foolproof. If you create a MERGE table from dissimilar MyISAM tables, you are very likely to run into strange problems.

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 non-unique index on the MERGE table, the index ordering is different for the tables if there was already a non-unique index in the underlying table. (This happens because ALTER TABLE puts UNIQUE indexes before non-unique indexes to facilitate rapid detection of duplicate keys.) Consequently, queries on tables with such indexes may return unexpected results.