A lightweight deduplication system can perform resource efficient data deduplication using an extent index and a content index. The extent index can store full fingerprints of data segments to be deduplicated and the content index can store shortened versions of the full fingerprints. The system can alternate between the extent and content indexes, and cache portions of the indices to perform lightweight data deduplication. Further, the system can be configured with an efficient heuristic approach for selecting content index data lookups for chains of volumes for deduplication, such as a long chain of snapshots.