MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5-end of miRNA and the target mRNA 3-UTRs is essential for the miRNA:mRNA recognition. Recent studies show that many seed matches in 3-UTRs, which are fully complementary to miRNA 5-ends, are highly conserved. Based on these features, a two-stage strategy can be implemented to achieve the de novo identification of miRNAs by requiring the complete base-pairing between the 5-end of miRNA candidates and the potential seed matches in 3-UTRs.