microRNA (miRNA) gene clusters are a group of miRNA genes clustered within a proximal distance on a chromosome. Although a large number of miRNA clusters have been uncovered in animal and plant genomes, the functional consequences of this arrangement are still poorly understood. Located in a polycistron, the coexpressed miRNA clusters are pivotal in coordinately regulating multiple processes, including embryonic development, cell cycles and cell differentiation. In this review, based on recent progress, we discuss the genomic diversity of miRNA gene clusters, the coordination of expression and function of the clustered miRNAs, and the evolutionarily adaptive processes with gain and loss of the clustering miRNA genes mediated by duplication and transposition events.