A storage system performing data deduplication includes a storage device configured to store data received from a host, and a controller configured to receive the data and an index associated with the data received from the host. The controller includes a memory configured to store mapping information and a reference count, the mapping information associating the index received from the host with a physical address of the storage system, the reference count associated with the index received from the host. The controller determines whether the data received from the host corresponds to a duplicate of data previously stored in the storage device by reading, from the memory, the mapping information and the reference count, the reading based on the index received from the host. The controller performs a deduplication process by updating the reference count if the data received from the host corresponds to the duplicate of data previously stored.