is it possible to do the Merge Replication in databases that having two different database structures ?
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Do you mean the database has different objects (tables, stored procedures, etc.) - yes definitely. Merge replication is only based on the tables in replication so tables outside that have no impact. You cannot however have differences in the table schema for tables that are replicated. You can have indexes, triggers, etc. different though on those tables (although it may cause replication issues).

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