AbstractCapparis spinosa L. is a perennial shrub and drought‐resistant plant and is well adapted to Mediterranean Ecosystem. Seventeen populations of caper, belonging to different bioclimatic zones, were assessed by morphological descriptors including nine parameters of seed (seed colour, major, medium and minor axial dimension, thousand seed mass, arithmetic mean diameter, geometric mean diameter, surface area and sphericity). The data underwent an analysis of variance, principal coordinate's analysis (PCO) and hierarchical classification analysis (HCA). Results showed that the dimensions of the major, medium and minor axes varied from 2.79 to 3.94 mm, 2.30 to 3.17 mm and 1.66 to 2.36 mm, respectively. The arithmetic and geometric mean diameters ranged, respectively, from 2.66 to 3.16 mm and from 2.19 to 3.05 mm. The sphericity and surface area ranged from 0.38 to 0.40 and from 1.20 to 1.24 mm2, respectively. The thousand seed mass varied from 4.71 to 12.05 g. The analysis of variance of studied descriptors showed significant differences according to the population. Both PCO and HCA generated from Gower general similarity coefficient among all populations showed two distinct clusters each corresponding to one subspecies. Grouping of populations did not reflect bioclimatic patterns, indicating specific adaptation of population to local environments. The divergence between the two caper subspecies (C. spinosa subsp. spinosa and C. spinosa subsp. rupestris), based on morphological traits, corroborates their taxonomic status.