In spite of its large lattice mismatch, Bi grows epitaxially in (111) orientation and almost free of defects on Si substrates. On Si(111), the Bi film is under compressive strain of less than 2% and shows a 6–7 registry to the Si(111)-(7 × 7) substrate. On Si(001), the compressive lattice strain of 2.3% results in the formation of an array of misfit dislocations with a periodicity of 20 nm. We studied the cooling process of ultrathin bismuth films deposited on Si(111) and Si(001) substrates upon excitation with short laser pulses. With ultrafast electron diffraction, we determined the thermal boundary conductance σK from the exponential decay of the transient film temperature. Within the error bars of 7%, the experimentally determined thermal boundary conductances are the same for both substrates and thus independent of the presence of a periodic array of misfit dislocations and the different substrate orientation.