The difference of gene expression between sclerotia-producing and non-sclerotia-producing single spore isolates from Morchella conica were preliminary analyzed by mRNA differential display reverse transcription-polymerase chain reaction (RT-PCR) technique and 67 differential gene fragments were obtained. Fifty-eight of their second PCR products were cloned and sequenced. Thirteen special differential gene fragments related to sclerotial formation were validated by semi-quantitative RT-PCR. Some gene fragments had certain homologies with lipoprotein, cyclin-dependent kinase C-3, glycerophosphoryl diester phosphodiesterase, Rho GDP-dissociation inhibitor, gamma-aminobutyrate permease, OmpA family protein, Transcript antisense to ribosomal RNA protein, sodium-calcium exchange protein and keratin-associated proteins 5, 6. In addition, the putative protein of some DNA fragments had higher similarity with hypothetical protein-coding gene in NCBI database, as well as some were only putative gene fragments. All these fragments were speculated to be the functional gene associated with sclerotial formation in morel.