Regulation of gene transcription and post-transcriptional processes is critical for proper development, genome integrity, and stress responses in plants. Many genes involved in the key processes of transcriptional and post-transcriptional regulation have been well studied in model diploid organisms. However, gene and genome duplication may alter the function of the genes involved in these processes. To address this question, we assayed the stress-induced transcription patterns of duplicated gene pairs involved in RNAi and DNA methylation processes in the paleopolyploid soybean. Real-time quantitative PCR and Sequenom MassARRAY expression assays were used to profile the relative expression ratios of eight gene pairs across eight different biotic and abiotic stress conditions. DNA methylation and RNAi pathway genes were more responsive to stress than the canonical miRNA pathway genes such as Dicer-like 1 (DCL1) and double-stranded RNA binding protein 1 (DRB1). The dicer-like 2 (DCL2) gene pair exhibited the most dramatic alterations in response to some stress conditions, indicating that this tandem gene pair may play an important role in the control of adaptive stress in soybean.