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The three species belonging to the sect. Dendrotelis of the genus Medicago: M. arborea L., M. citrina (Font Quer) Greuter, and M. strasseri Greuter, Matthas & Risse, were characterized using 12 morphometrical characters of seeds and 20 of seedlings. These species have interest for the regeneration of degraded lands in semi-arid climates. M. arborea presents the largest phenotypic variability and is dispersed throughout the Mediterranean basin, while the other two species are endemic to a very reduced area, M. citrina, in Columbretes Islands and Cabrera Islands (Spain) and M. strasseri in Crete. Several populations of M. arborea were measured, in order to compare the intraspecific variability within M. arborea with the differences among all three species. The multivariate analysis of the data used characters that were independent of the size of the studied organs. The three species were clearly differentiated on the basis of seed characters. On the other hand, seedling characters distinguished M. citrina from the other two species, but M. strasseri and the populations of M. arborea were intermingled. In spite of this, we have described relevant morphological differences among M. arborea, M. strasseri and M. citrina, which are consistent with other ecological or bromatological differences. The study supports that the three accessions merit to be considered as three different species.