It has been shown recently that gold coated silica Janus particles can cluster when subject to a smooth optical field due to the presence of an attractive interaction of hydrodynamic nature (1). Such an interaction comes from the simultaneous presence of various factors: the thermophoretic flow around the Janus particle itself by the temperature gradient due to the partial absorption of the optical intensity on the gold cap of the particle, the presence of a boundary near the particle, the particular orientation (cap down) due to the gravity and the distinctive property of silica particles in water to move from colder to hotter regions. The model presented in the article suggests that there are various possibilities for driving the behaviour of the system: if the material constituting the particle had opposite thermophoretic features (particle moving from hotter to colder regions) then the sign of the hydrodynamic interaction would be reversed and we wouldn’t observe any tendence to form clusters. In this study we investigate the two cases stated above: we compared the behaviour of gold coated silica Janus particles with the behaviour of gold coated polystyrene Janus particles under the effect of a Gaussian optical potential, for two different kind of boundaries (glass slide, polymer slide). We find that in the case of polymer slide there is evidence of a repulsive hydrodynamic interaction among gold coated polystyrene Janus particles, which is less pronounced for gold coated silica Janus particles. Moreover, the interplay of optical forces and repulsive hydrodynamic interaction is such that, in case of a mixed solution with Janus colloids and normal colloids, we obtain a relatively fast separation of the two species, that might find applications for particles sorting. Though relatively simple in the experimental realisation, this study shows how varied can be the interplay of different effects of different nature, i.e., due to external fields (optical, thermophoretic, hydrodynamic forces related to the beam itself) and due to the self-generated field (thermophoretic, hydrodynamic interaction due to the absorption by the gold cap). Understanding and engineering the experimental conditions might lead to realise systems where one can switch from clustering to sorting, opening possibilities for the realisation of reconfigurable colloidal structures, that might be interesting for cargo deliveries, or the realisation of micro-rotors.