Suppose you have two mysql instances c:\mysq1 and c:\mysql2 1- create file c:\mysql1\my.cnf add the following lines [mysqld] datadir = C:/mysql1/data port = 3308 2- create file c:\mysql2\my.cnf add the following lines [mysqld] datadir = C:/mysql2/data port = 3309 3-now run the first instance cd c:\mysql1\bin mysqld --defaults-file=c:\mysql1\my.cnf 4-open another command and run the second instance cd c:\mysql2\bin mysqld --defaults-file=c:\mysql2\my.cnf finsihed ;)