Estrogens are steroid hormones that have been implicated in a variety of cellular and physiological processes, in the development of diseases such as cancer and are also known to be associated with the effects of endocrine disrupting chemicals. Here we show that 17-estradiol (E₂) alters microRNA (miRNA) expression profiles in the adult zebrafish (Danio rerio). An association between E₂ and the expression of 25 miRNAs was found 12 hours after treatment. Among the most up-regulated miRNAs were miR-196b and let-7h and the most down-regulated miRNAs included miR-130c and miR-101a. Tissue specific changes in the transcripts levels of estrogen receptors (Esr1, Esr2a and Esr2b) and of miRNAs were found after hormone treatment. The most up-regulated miR-196b and its precursors are highly expressed in the skin and showed similar tissue specific expression patterns after treatment, indicating a common pattern of regulation by E₂. MiR-196b was shown to fine-tune the expression of its target gene Hoxb8a after treatment in whole body homogenates. Taken together, our results suggest a novel pathway for the multifunctional and pleiotropic effects of estrogens and open new directions for future investigations of their association with miRNAs involved in estrogen regulated physiological processes and diseases.