We present the calculations of the linear thermopower in single electron molecular transistors. The molecule with its vibrational internal degrees of freedom used as central object in a single electron transistor can in some cases be characterised by negative effective charging energy. This allows to model the system by Anderson Hamiltonian with negative U. Here we extend the previous calculations of the conductance of such system and study the linear thermopower of a dot characterised by negative value of the on-dot interaction U. We focus on the weak tunnelling limit, for which a rate equation approach is valid.