Context. The study of the motion of the members of a given open cluster or stellar association provides key information about their formation and early evolution. The Chamaeleon cloud complex constitutes one of the closest and best studied low-mass star-forming regions in the Galaxy. Aims. We want to provide further evidence of the origin of the proposed stellar members of Chamaeleon and to identify interlopers from the foreground Cha and η Cha associations. Methods. We have compiled lists of spectroscopically confirmed members of Chamaeleon I and II, Cha and η Cha, and of background objects in the same line of sight. Using Virtual Observatory tools, we cross-match these lists with the UCAC3 catalogue to get the proper motions of the objects. In the vector point diagram, we identify the different moving groups, and use this information to study the membership of proposed candidate members of the associations from the literature. For those objects with available radial velocities, we compute their Galactic space velocities. We look for correlations between the known properties of the objects and their proper motions. Results. The members of the dark clouds exhibit clearly different proper motions from those of the foreground associations and of the background stars. The data suggest that Chamaeleon II could have different dynamical properties from Chamaeleon I. Although the two foreground clusters and η Chamaeleontis constitute two different proper motion groups, they have similar spatial motions, which are different from the spatial motion of Chamaeleon I. On the other hand, the space motions of the Chamaeleon II stars look more similar to those of the foreground clusters than to the Chamaeleon I stars, but the numbers are low. We find no correlations between the proper motions and the properties of the objects in either of the clouds. Conclusions. On the basis of proper motion, Chamaeleon I and II constitute two physical entities unrelated to the foreground and η Chamaeleontis clusters, but with the available data it is unclear to what extent the stellar populations in both clouds are physically connected to each other.