This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a tangible AR environment were able to complete the task of identifying molecular structures more quickly and accurately than those with a typical desktop-PC environment using a Web browser. A usability test by participants who learned molecular structures and answered relevant questions demonstrates that the environments had no effect on their learning of molecular structures. However, a preference test reveals that learners preferred a more tangible AR environment to a Web-browser environment in terms of overall enjoyment, reality of manipulation, and sense of presence, and vice versa in terms of ease of viewing, experience, and durability.