MicroRNAs (miRNAs) are the central component of an important layer of post-transcriptional regulation of gene expression. In plants, miRNAs target the transcripts in a manner that is generally highly sequence complementary. Extensive research is being made to study the genome-wide miRNA-mediated regulation of gene expression, which has resulted in the development of many tools for an in-silico prediction of miRNA targets. Although several tools have been developed for predicting miRNA targets in model plants, genome-wide analysis of miRNA targets is still a challenge for non-model species that lack dedicated tools. Here, we describe a computational procedure for studying miRNA-mediated interactions in plants, which is based on the fact that canonical miRNA target sites are highly complementary, the miRNAs negatively regulate the expression of their target genes and that miRNAs may form regulatory networks as one miRNA may target more than one transcript and vice-versa to modulate and fine-tune expression of the genome.