MicroRNAs (miRNAs) are small non-coding RNA which generate from large hairpin precursors and play important role on post-transcriptional regulators of target genes. Although, many individual miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in trematode. By the method of using high throughput Solexa sequencing technology, 11.02 million clean reads have been obtained of Paragonimus westermani. Among the clean reads, 1.14 million ones (10.37%) were perfectly mapped onto the S. japonicum genome which included 20,322 (0.69%) unique sequences. A number of 9,492,613 (86.17%) reads had no match with public databases and marked as un-annotated RNAs. Nucleotide bias analysis found that the known miRNAs showed high bias and the guanine was the dominant nucleotide, particularly at the 2nd and 23rd positions which were almost at the beginning and end of conserved miRNAs. Three novel miRNA corresponding to 18 precursors were predicted. To the knowledge, this is the first report of miRNA profiles in P. westermani which will contribute to better understanding of the complex biology of this zoonotic parasite. The reported data of P. westermani miRNAs should provide valuable references for miRNA studies of closed related zoonotic trematode.