Chemistry deals with concepts associated with non-observable entities. Using analogies may facilitate the learning of such concepts, including the atom. In this study, we investigated the analogies that two chemistry teachers used when teaching about the atom at two Mozambican universities. These analogies were characterized and the reasons that led teachers to use analogies were analyzed. Teachers were observed when teaching about the atom and they were interviewed afterwards. Both teachers used different amounts of analogies, which focused on the Thomson and the Rutherford models. Almost all the analogies, that were created and used spontaneously, showed a lack of internal consistency, which may reduce their didactical value and even make them inducing incorrect ideas in the students. Teachers stated that they would start planning the use of analogies in their classes. If they are to do this properly, they need training that integrates two components: analogies and chemistry.