The aim of this chapter is to describe how microarrays can be used to identify miRNAs that participate in fruit development in a non-model plant: prickly pear (Opuntia spp). Here, we describe a technology including molecular biology and bioinformatics methods combined to identify, select, and isolate candidate miRNAs putatively involved in prickly pear development. We describe how miRNA expression analysis through microarray hybridization was performed and the expression of selected miRNAs validated using RT-PCR.