The present study analysed archaeological pottery in the early Yayoi period of the prehistoric Japanese archipelago, i.e. Ongagawa style pottery, which has been traditionally regarded as an indicator of the spread of rice farming in the archipelago. To this end, we quantified the two- and three-dimensional data of outlines and surfaces of the pottery, based on elliptic Fourier and spherical harmonics analyses, respectively. The results show morphological variation is spatially and temporally structured, consistent with an archaeological view that the pottery style spread via two routes (the Japan Sea route and Setouchi route) with the potential of more complex interactions between the transmission routes. The present study exemplifies a useful quantitative method to theorize cultural evolutionary trajectories of archaeological remains.