MicroRNAs are small non-coding RNAs of approximately 22 nt with important regulatory roles in post-transcriptional regulation of gene expression. To date, no miRNAs have been reported in plant pathogenic fungi. Here we used Solexa sequencing to find new miRNAs in a plant pathogenic fungus Sclerotinia sclerotiorum. 13,229,401 high-quality reads were obtained, a total of 5,645,718 reads were mapped to the S. sclerotiorum genome corresponding to 348,108 unique sRNAs. Among the sRNAs, 2 microRNA-like RNAs (milRNAs) and 42 mil-RNA candidates were identified by sequence analysis. Northern blot and RT-PCR results showed that some milRNAs and candidates are differentially expressed in sclerotial development suggesting the role of these milRNAs and candidates in this biological process. Our results provide new insights into the functional roles of small RNAs and add new resources for the study of plant pathogenic fungi.