Techniques for deduplicating a data stream with checksum data embedded therein are described. According to one embodiment, a first data stream is received from a client having a plurality of data regions and a plurality of checksums for verifying integrity of the data regions embedded therein, where the first data stream represents a file or a directory of one or more files of a file system associated with the client. In response the first data stream with the checksums removed is deduplicated into a plurality of deduplicated chunks.