AbstractAims, including the rationaleSalinity and drought are the two major stresses limiting the productivity of economically important crops such asGlycine max(soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NACmodule has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NACmodule in salt stress in soybean is not fully understood.MethodsIn this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets.Key resultsIt was found that four salt stress deregulated miRNAs targeted theNACtranscription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (−2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co‐expression assay validated that gma‐miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC‐TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions.Main conclusionCollectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC‐TFmodule may play an important role in determining the adaptive response of plants to stress.