Provided are a method, system, and article of manufacture for managing metadata for data blocks used in a deduplication system. File metadata is maintained for files having data blocks in a computer readable device. Data block metadata is maintained for each data block in the computer readable device. The data block metadata for one data block includes a data block reference and content identifier identifying content of the data block. The file metadata for each file includes the data block reference to each data block in the file. A determination is made of an unreferenced data block in the computer readable device that has become unreferenced. Indication is made that the data block metadata for the determined unreferenced data block as unreferenced metadata. The data block reference of the unreferenced metadata is maintained in the computer readable device in response to determining that a includes the data block indicated in the unreferenced metadata.