Embodiments presented herein describe techniques for deduplicating chunks of data across multiple clusters. A process executing in a storage system identifies one or more chunks in an incoming stream of data. For each chunk, a first fingerprint corresponding to the chunk is generated. The process determines whether the first fingerprint matches a second fingerprint listed in a corresponding entry in a deduplication map. Each entry of the deduplication map corresponds to a chunk stored in a location in one of the storage clusters. Upon determining that the first fingerprint matches the second fingerprint, the process writes, to a local persistent storage, a pointer referencing the location in that storage cluster.