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Calligonum spp. are common plant species in desert areas of central Asia. Since they are drought-resistant, salt-tolerant and grow successfully in sand, they are useful for wind-breaks and dune stabilization. The fruit morphology is regarded as a key taxonomic character for the genus. Morphological variation among individuals and populations of Calligonum mongolicum Turcz. and C. pumilum Losinsk. is investigated in the present paper. The chromosome number for both species is also presented and found to be the same (2n=18). By combining the overlap and variation in morphological characters, the similar variational ranges and complex relationships of fruit characters, we suggest that C. pumilum should be merged with C. mongolicum and we further discuss additions and improvements to the description of C. mongolicum in ’Flora of China’.