It is known that vegetation plays an important role in the retention of heavy metals in salt marshes by taking up and accumulating the metals. In this study, we investigated whether arbuscular mycorrhizal fungi (AMF) increase Cd and Cu uptake and accumulation in the root system of the salt marsh species Aster tripolium L., and whether indigenous AMF isolated from polluted salt marshes have higher capacity to resist and alleviate metal stress in A. tripolium than isolates of the same species originated from nonpolluted sites. Plants inoculated with Glomus geosporum, either isolated from a polluted salt marsh site (PL isolate) or from a non-polluted site (NP isolate), and non-mycorrhizal (NM) plants were compared in a pot experiment at four different Cd and Cu concentrations. Cd had no effect in root colonization, whereas high concentrations of Cu decreased colonization level in plants inoculated with the NP isolate. AM colonization did not increase plant dry weight or P concentration but influenced root Cd and Cu concentrations. Inoculation with PL and NP isolates enhanced root Cd and Cu concentrations, especially at highest metal addition levels, as compared to NM plants, without increasing shoot Cd and Cu concentrations. There was no evidence of intraspecific variation in the effects between AMF isolated from polluted and non-polluted sites, since there were no differences between plants inoculated with PL or NP isolate in any of the tested plant variables. The results of this study showed that AMF enhance metal accumulation in the root system of A. tripolium, suggesting a contribution of AMF to the sink of metals within vegetation in the salt marshes.