The sequences of the internal transcribed spacer (ITS) regions of ectomycorrhizal fungi collected from Sichuan Province were analyzed using a PCR primer pair specific to T. matsutake. The amplified fragments were sequenced and compared with each other to build a phylogenetic tree. The mRNA deep sequencing approach was adopted to identify differentially expressed T. matsutake genes among the transcriptomes developed from a Xiaojin sample. A phylogenetic analysis of the aligned sequences was performed using maximum-likelihood (ML) and neighbor-joining (NJ) analyses. The results clearly showed that the KD (KM657344) and BT (KM657342) strains were more closely related to each other than to other strains. Moreover, T. matsutake from Sichuan differed from those specimens derived from Heilongjiang, Yunnam, and Guizhou provinces of China, Finland, and Japan. Furthermore, there was extremely high homology among these T. matsutake samples, despite some genetic variation. In addition, the genome of T. matsutake was sequenced using Illumina sequencing technology (RNA-seq). In all, a total of 24,549,990 reads were obtained that yielded 18,266,492 high-quality clean reads. The quality reads were excluded later. The BLAST analysis of the sequence reads against the NR database indicated that T. matsutake shared a high number of contigs with Laccaria bicolor. The results also indicated that catalytic activity, metabolic processes, metabolic pathways, and biosynthesis of secondary metabolites were the main functions identified by gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Phylogenetic analysis showed that T. matsutake growing in Sichuan differed from samples growing in other regions. The differences in secondary metabolites between the Sichuan and Xiaojin samples may be due to differences in metabolic pathways. Thus the study provides a foundation for understanding T. matsutake biogeography and origins, and identifies DEGs in the Xiaojin sample to help elucidate the molecular mechanisms in secondary metabolite synthesis.