Recently there has been growing interest in characterising population structure in cultural data in the context of ongoing debates about the potential of cultural group selection as an evolutionary process. Here we use archaeological data for this purpose, which brings in a temporal as well as spatial dimension. We analyse two distinct material cultures (pottery and personal ornaments) from Neolithic Europe, in order to: a) determine whether archaeologically defined “cultures” exhibit marked discontinuities in space and time, supporting the existence of a population structure, or merely isolation-by-distance; and b) investigate the extent to which cultures can be conceived as structuring “cores” or as multiple and historically independent “packages”. Our results support the existence of a robust population structure comparable to previous studies on human culture, and shows how the two material cultures exhibit profound differences in their spatial and temporal structuring, signalling different evolutionary trajectories.