In order to investigate genetic diversity and population structure of Ceratoides arborescens, six populations were selected from different steppe types in Inner Mongolia grasslands of China. Inter-simple sequence repeat (ISSR) markers were used to assess the genetic diversity within and among natural populations of C. arborescens. Thirteen ISSR primers generated 154 discernible DNA bands, of which 151 (98.05%) were polymorphic. High genetic diversity was detected at the species level [percentage of polymorphic loci (PPB) = 98.05%; H = 0.2984; I = 0.4557], whereas, relatively low genetic diversity existed within populations (PPB = 80.62%; H = 0.2675; I = 0.4031). Analysis of molecular variance showed that variation existed mainly within populations (73.25%) rather than among populations (26.75%), which was in line with the high level of gene flow (Nm = 4.3332). The Mantel test found no significant correlation between genetic distance and geographic distance (r = 0.7522, P < 0.05). Six populations were clustered into two main groups, a desert steppe group and a typical steppe group.