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Background    Senna obtusifolia  and  Senna occidentalis  (Leguminosae), whose seeds have similar appearance and chemical constituents, are easily confused in using their seeds. To elucidate the similarities and differences between  S. obtusifolia  seeds and  S. occidentalis  seeds, three molecular markers and high performance liquid chromatography (HPLC) were employed to evaluate the seeds characteristics of these two medicinal herbs.    Results  The results showed that selected 3 ISSR and 7 SCoT primers could distinguish  S. obtusifolia  seeds from  S. occidentalis  seeds based on the specific band and UPGMA dendrogram. ITS2 sequence indicated that the intra-specific similarity of 20  S. obtusifolia  and 16  S. occidentalis  was 99.79 and 100.0%, respectively, while the inter-specific similarity between  S   . obtusifolia  and  S. occidentalis  was 89.58%. Although phylogenetic analysis revealed that these two species had a close relationship, they were assigned to different branches. HPLC fingerprint results showed that seeds of  S. obtusifolia  and  S. occidentalis  shared some secondary metabolites, but aurantio-obtusin was not detected in  S. occidentalis  seeds which could differentiate  S. obtusifolia  seeds from  S. occidentalis  seeds.    Conclusions  The present study not only compared the seeds characters of  S. obtusifolia  and  S. occidentalis  from molecular and secondary metabolites levels, but also provided a convenient method to identify  S. obtusifolia  seeds and  S. occidentalis  seeds effectively.    Electronic supplementary material  The online version of this article (doi:10.1186/s40529-017-0196-4) contains supplementary material, which is available to authorized users.

Identification of seeds based on molecular markers and secondary metabolites in Senna obtusifolia and Senna occidentalis