For a storage apparatus where flash memory disks and hard disks coexist, high-density mounting of flash memory modules is achieved. The storage apparatus includes flash memories and a storage controller. A second storage apparatus including magnetic disks is connected to the storage apparatus. The storage controller can form a storage area using a flash memory or a magnetic disk to create a logical volume. When an input/output request is issued from a host computer, if a storage area is formed with a flash memory, the storage controller directly accesses the flash memory to handle the request. When the storage apparatus defines a storage area formed with a flash memory, the storage apparatus defines the storage area by adding up the capacity of a storage area to be provided for the host computer and a substitute area capacity determined in consideration of restrictions on the number deletions of the flash memory.