Five Calligonum species endemic to the Tarim Basin - C. roborowskii, C. kuerlese, C. juoqiangense,C. yengisaricum, and C. taklimakanense - were compared using 14 morphological characteristics and nrDNA ITS and cpDNA trnL-F molecular data. Intraspecific and interspecific morphological variation was uncovered, with variation between species significant for most characteristics. Based on Euclidean distances, C. roborowskii and C. kuerlese were the most similar, and C. yengisaricum and C. kuerlese were the most divergent. There was very little variation in the molecular sequence data: although several variable sites were present in ITS and trnL-F regions, none of them were parsimony informative. Results of morphological and molecular analyses suggest that the various morphological characteristics of the studied Calligonum species are strongly shaped by environmental factors, with the observed intraspecific and interspecific morphological variation a product of the spatial isolation and extreme drought of the Tarim Basin.