The effect of geographical isolation on the inter- and intra-specific seed variability of the Astragalus tragacantha complex was investigated by using a computer-aided imaging system. In particular, seed morphometric and colorimetric features of Astragalus balearicus, A. tegulensis, A. terraccianoi, A. thermensis and A. tragacantha were measured and the data were used to discriminate among regions of provenance, taxa and populations. Discriminant analysis of the data supports the accepted taxonomy of the group and the hypothesis that interspecific differentiation resulted from geographical isolation. The results also showed a positive correlation between the wideness of species’ distribution and the levels of seed intra-specific variability.