Yes, they are different and should be marked as such. For my thesis, I am required to have both a list of works cited and an annotated bibliography. As mentioned, the list of works cited (reference list) should only contain references that match-up to citations in the text.
Additionally, my thesis also has an annotated bibliography as an appendix. Essentially this is where I can place works which may have influenced my paper, but may not necessarily have been cited in the text. Each entry also has an annotation describing how it is relevant to the paper itself.
An example of this, is that one of the books (which I read while doing research for my thesis) provided insight I used to prototype the testing framework for my project. I did not end up actually using anything from the book for the written portion. But, it did influence the project overall. Therefore I put it in my annotated bibliography, but not in my list of works cited.