This work aims to discriminate among different species of the genus Cistus, using seed parameters and following the scientific plant names included as accepted in The Plant List. Also, the intraspecific phenotypic differentiation of C.creticus, through comparison with three subspecies (C.creticus subsp. creticus, C.c.subsp. eriocephalus and C.c. subsp. corsicus), as well as the interpopulation variability among five C.creticus subsp. eriocephalus populations was evaluated. Seed mean weight and 137 morphocolorimetric quantitative variables, describing shape, size, colour and textural seed traits, were measured using image analysis techniques. Measured data were analysed applying step-wise linear discriminant analysis. An overall cross-validated classification performance of 80.6% was recorded at species level. With regard to C. creticus, as case study, percentages of correct discrimination of 96.7% and 99.6% were achieved at intraspecific and interpopulation levels, respectively. In this classification model, the relevance of the colorimetric and textural descriptive features was highlighted, as well as the seed mean weight, which was the most discriminant feature at specific and intraspecific level. These achievements proved the ability of the image analysis system as highly diagnostic for systematic purposes and confirm that seeds in the genus Cistus have important diagnostic value.