MicroRNAs (miRNAs) represent a newly identified class of non-protein-coding ~20 nt small RNAs which play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. After searching a genomic survey sequence database using homologs and secondary structures, we found many cotton miRNAs belonging to several miRNA families. More than 50 potential targets were identified for these miRNAs based on the fact that miRNAs exhibit perfect or nearly perfect complementarity with their target sequences. A majority of the targets are transcription factors which play important roles in cotton development, including leaf, shoot, and root development. Additionally, these cotton miRNAs are also involved in other cellular processes, such as fiber development, signal transduction, stress response, sucrose and cellulose synthesis, and ubiquitin protein degradation pathway. Some of the newly identified miRNA targets may be unique to cotton.