Several studies have compared seed banks of the different morphs of heteromorphic species, but none of them was on an amphi-basicarpic species. Our primary aim was to compare the relative ability of aerial and basal diaspores of an amphi-basicarpic species to form a seed bank. We compared the seed-bank dynamics of basal and aerial diaspores of three populations of the cold-desert annual Ceratocarpus arenarius growing in the Junggar Desert in north-western China. A 2.5-year experimental garden study compared germination phenology and retention of viability in basal (a) and aerial (c and f) morphs. Aerial morphs formed a modified Thompson and Grime type III seed bank (small proportion of seeds carried over to next year) and the basal morph a modified type IV seed bank (large proportion of seeds carried over to next year). Seeds germinated only in spring, and cumulative germination percentages were f>c>a (year 1), f = c>a (year 2) and f = c = a (year 3). The relationship between length of germination period, retention of viability during burial and relative ability to form a persistent seed bank was basal morph > aerial morphs. The results of this seed-bank study on C. arenarius are in full agreement with those published previously on seed dispersal and dormancy in this species. Thus, strong additional support is provided for a high risk–low risk germination strategy in this cold-desert annual.