Methods and apparatus for network efficient deduplication

Mechanisms are provided for performing network efficient deduplication. Segments are extracted from files received for deduplication at a host connected to a target over one or more networks and/or fabrics in a deduplication system. Segment identifiers (IDs) are determined and compared with segment IDs for segments already deduplicated. Segments already deduplicated need not be transmitted to a target system. References and reference counts are modified at a target system. Updating references and reference counts may involve modifying filemaps, dictionaries, and datastore suitcases for both already deduplicated and not already deduplicated segments.