Web annotation is a Web 2.0 technology that allows learners to work collaboratively on web pages or electronic documents. This study explored the use of Web annotation as an online discussion tool by comparing it to a traditional threaded discussion forum. Ten graduate students participated in the study. Participants had access to both a Web annotation tool and a threaded forum when having discussion on a given topic and were free to use either tool or both to post their comments. A case study method was adopted. The analysis of participant posts and participant survey responses showed that both the threaded forum and the Web annotation tool successfully supported interactions and knowledge construction during the online discussion. The Web annotation tool had advantages in locating specific information on the websites and making content-specific discussions, and the discussion forum was more suitable for posting summarized comments. While participants were more likely to offer alternative or complementary views in the discussion forum, self-reflection was the major type of knowledge construction behavior when participants used the Web annotation tool.