Cadmium is one of the most harmful heavy metals that harm agricultural products. Evaluating microRNAs expression is a new and accurate method to study plant response in various environmental conditions. So this study aimed to evaluate the contribution of two symbiotic fungi in improving flax tolerance in a Cd-polluted soil using microRNAs and their target gene expression. A factorial pot experiment in a completely randomized design was conducted with different levels of Cd (0, 20, and 40 mg kg -1 ) on non-inoculated and inoculated flax with Claroideoglomus etunicatum and Serendipita indica . The results presented that increasing Cd levels caused a constant decline of alkaline phosphatase of soil (from 243 to 210 and 153 μg PNP g -1 h -1 ), respectively, from control (Cd0) to 20 and 40 mg Cd kg -1 . However, the inoculation of flax with fungi significantly enhanced these properties. A negative correlation was observed between the expression level of microRNA 167 and microRNA 398 with their corresponding target genes, auxin response factor 8 and superoxide dismutase zinc/copper 1, respectively. The expression level of both microRNAs and their targets indicated that the inoculation with symbiont fungi could diminish Cd stress and enhance the growth of flax.