BackgroundArmillariaspecies are plant pathogens, but a fewArmillariaspecies can establish a symbiotic relationship withGastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine.Armillariais a nutrient source for the growth ofG. elata. However, there are few reports on the molecular mechanism of symbiosis betweenArmillaria speciesandG. elata.The genome sequencing and analysis ofArmillariasymbiotic withG. elatawould provide genomic information for further studying the molecular mechanism of symbiosis.ResultsThe de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for theA. gallicaJzi34 strain, which was symbiotic withG. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes ofArmillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins betweenA. gallicaJzi34 and other fourArmillariawas complex.ConclusionsThese characteristics may be beneficial for establishing a symbiotic relationship withG. elata. These results explore the characteristics ofA. gallicaJzi34 from a genomic perspective and provide an important genomic resource for further detailed study ofArmillaria. This will help to further study the symbiotic mechanism betweenA. gallicaandG. elata.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09384-4.