In one embodiment, in response to a list of a plurality of fingerprints representing data chunks to be replicated from a source storage system to a target storage system over a network, one of the fingerprints is selected as a representative fingerprint that matches selection criteria. The source storage system generates a fingerprint representation for each of the fingerprints that is smaller than the corresponding fingerprint. The representative fingerprint and the fingerprint representations are transmitted to the target storage system over the network, without transmitting all full fingerprints of the data chunks, to allow the target storage system identifying which of the data chunks are missing. In response to information received from the target storage system indicating one or more data chunks that are missing at the target storage system, the missing data chunks are then transmitted to the target storage system.