Mechanisms are provided for improving the efficiency of garbage collection in a deduplication system by intelligently managing storage of deduplication segments. When a duplicate segment is identified, a reference count for an already maintained segment is incremented only if the already maintained segment has the same lifecycle as the identified duplicate segment. In some instances, an already maintained segment is assumed to have the same lifecycle if it is not stale or the age is not significantly different from the age of the newly identified duplicate. If the already maintained segment is has a different lifecycle, the new segment is stored again even though duplicates are already maintained.