Purpose Phytoremediation experiments were carried out to investigate the ability of two species of Salicornia persica and Salicornia perspolitana for the extraction of heavy metals including aluminum, iron and copper. In this study, manure and biochar were applied to improve phytoremediation performance. Methods The two species of S. persica and S. perspolitana were grown outdoor in experimental pots. The effect of experimental treatments including manure and biochar on the two species was investigated. Results The results showed that biochar significantly influenced (P <0.05) on the accumulation of heavy metals in both S.persica and S. perspolitana. In biochar treatment, the values of heavy metals in roots and shoots were found to be 3327 mg/kg, 109.17 mg/kg for aluminum, 3527 mg/kg and 142.17 mg/kg for iron, and 73.93 mg/kg and 11.90 mg/kg for copper, respectively. In the manure treatment, the values of heavy metals in the roots and shoots were reported as 3993 mg/kg and 119.29 mg/kg for aluminum, 5542 mg/kg and 179.17 mg/kg for iron and 78.67 mg/kg and 12.74 mg/kg for copper, respectively. Conclusions In general, the accumulation of heavy metals in S. perspolitana was higher than S. persica, and our results indicated that the use of biochar and manure caused stabilization of heavy metals in the soil and consequently reduced accumulation of heavy metals in both S. persica and S. perspolitana.