Small regulatory non-coding RNA molecules, known as micro RNAs, are potential regulators of gene expression at the post-transcriptional level. In Drosophila melanogaster microRNAs control important developmental processes such as cell division, neural development, and oogenesis. Here we present the first study on mosquito, Aedes aegypti, microRNAs as an initial step in understanding the intricate developmental processes underlying metamorphosis. To determine the temporal profile of mosquito microRNAs the miRCURY array chip was hybridized with larval and pupal mosquito cDNA probes. The microRNA transcription profiles identified ninety differentially expressed microRNAs of the 3845 tested. Studies of microRNAs in diverse insect species may provide important clues to better understand the natural selection of microRNA genes as well as their impact on biological functions in insects.