MicroRNAs (miRNAs) regulate gene expression at the post-transcription level in both animals and plants. Ultra deep sampling of small RNA libraries by next generation sequencing has provided rich information on the miRNA transcriptome of various plant species. We developed miRDeep-p which employs the signature distribution of small RNA reads along the miRNA precursor as a model in plants to profile expression of known miRNA genes and to identify novel ones. Taking advantage of miRDeep-p, we utilize more than 80 small RNA liberaries from 16 plant species to annotate, profile and compare the expressed miRNA genes. Totally, more than 600 conserved and 1,500 nonconserved miRNA genes were detected in these species. Of them, some new miRNAs and their expressed profiles in Arabidopsis have been validated by other experimental methods.