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MicroRNAs are small non-coding RNA molecules 20–24 nucleotides long, found in plants, animals, and some viruses, which participate in the transcriptional and post-transcriptional regulation of gene expression through RNA interference. The first microRNAs were described in the early 1990s, but they began to be considered as a separate class of biological regulatory molecules with specific functions in the early 2000s. In plants, microRNAs play an important role in responses to biotic and abiotic stress and control a wide range of physiological processes, including nutrition, growth, and interactions with other organisms by modulating the expression of transcription factors, stress-inducible proteins, and other genes. With the discovery of microRNAs, there was a need to develop methods for their reliable identification and quantification, since the classical approaches proved to be ineffective due to the short length, low expression level, and high variability of these molecules. In this article, we present a systematic review of the main methods for studying microRNA, such as quantitative reverse transcription PCR (RT-qPCR), Northern blot hybridization, microRNA library creation followed by high-throughput sequencing, as well as their modifications.