Layered crystals are known to be good candidates for bulk thermoelectric applications as they open new ways to realise highly efficient devices. Two dimensional materials, isolated from layered materials, and their stacking into heterostructures have attracted intense research attention for nanoscale applications due to their high Seebeck coefficient and possibilities to engineer their thermoelectric properties. However, integration to thermoelectric devices is problematic due to their usually high thermal conductivities. Reporting on thermal transport studies between 150 and 300 K, we show that franckeite, a naturally occurring 2D heterostructure, exhibits a very low thermal conductivity which combined with its previously reported high Seebeck coefficient and electrical conductance make it a promising candidate for low dimensional thermoelectric applications. We find cross- and in-plane thermal conductivity values at room temperature of 0.70 and 0.88 W m−1 K−1, respectively, which is one of the lowest values reported today for 2D-materials. Interestingly, a 1.77 nm thick layer of franckeite shows very low thermal conductivity similar to one of the most widely used thermoelectric material Bi2Te3 with the thickness of 10–20 nm. We show that this is due to the low Debye frequency of franckeite and scattering of phonon transport through van der Waals interface between different layers. This observation open new routes for high efficient ultra-thin thermoelectric applications.