We report a combined experimental (C-AFM and SThM) and theoretical (DFT) study of the thermoelectric properties of molecular junctions made of self-assembled monolayers on Au of thiolated benzothieno-benzothiophene (BTBT) and alkylated BTBT derivatives (C8-BTBT-C8). We measure the thermal conductance per molecule at 15 pW/K and 8.8 pW/K, respectively, among the lowest values for molecular junctions so far reported (10-50 pW/K). The lower thermal conductance for C8-BTBT-C8 is consistent with two interfacial thermal resistances introduced by the alkyl chains, which reduce the phononic thermal transport in the molecular junction. The Seebeck coefficients are 36 μV/K and 245 μV/K, respectively, the latter due to the weak coupling of the core BTBT with the electrodes. We deduce a thermoelectric figure of merit ZT up to ca. 1E-4 for the BTBT molecular junctions at 300K, on a par with the values reported for archetype molecular junctions (olygo(phenylene ethynylene) derivatives).