Provided are a computer program product, system, and method for merging entries in a deduplication index. An index has chunk signatures calculated from chunks of data in the data objects in the storage, wherein each index entry includes at least one of the chunk signatures and a reference to the chunk of data from which the signature was calculated. Entries in the index are selected to merge and a merge operation is performed on the chunk signatures in the selected entries to generate a merged signature. An entry is added to the index including the merged signature and a reference to the chunks in the storage referenced in the merged selected entries. The index of the signatures is used in deduplication operations when adding data objects to the storage.