Objective：This study aims to discover the characteristics of gene mutation and gene expression profile of primary adenoid cystic carcinoma（ACC） and mucoepidermoid carcinoma（MEC） in the lungs by sequencing. Methods：Total 14 cases of lung ACC and 24 cases of lung MEC were enrolled. Samples of tumor tissues and adjacent tissues were collected. After extracting DNA and RNA，DNA and RNA transcription group were used to gene sequencing and bioinformatics analysis. Results：Among the detected DNA mutations in cancer tissues，MYB/MYBL1 fusion was detected in 78.5%（11/14） lung ACC patients. The most common mutation in lung MEC patients was MAML2 rearrangement，and 3 MEC patients had EWSR1 fusion，and 1 case ROS1 fusion occurs in MEC patients. Among the RNA differential genes in cancer tissues and adjacent tissues，SOX10 and BCL11A are highly expressed in lung ACC，and the most differentially expressed gene in lung MEC is TFAP2A. Conclusion：SOX10 and BCL11A may become new biomarkers of lung ACC. TFAP2A is related to lung MEC resistance to anlotinib.