miR-196a is located in the posterior trunk and plays a role in limb development. Here we show that miR-196a is able to induce eye anomaly in Xenopus laevis. Microinjection of synthetic miRNA precursor molecule for mammalian miR-196a into Xenopus embryo is sufficient for miR-196a overexpression during early development. The misexpression of miR-196a in anterior embryo led to dose-dependent eye anomalies, especially size reduction. In addition, the expression of ET, Rx1, Six3, Pax6, Lhx2, Optx2 and Ath5 in eye field or optic cup was also down-regulated. These results indicate that miR-196a can target gene(s) in the genetic network involved in eye formation, providing a potential tool for studying the mechanisms of eye development and diseases.