<h3>Study Objective</h3> To identify the difference in molecular mechanisms between ovarian endometrioma (OMA) and deep endometriosis (DE). <h3>Design</h3> N/A. <h3>Setting</h3> N/A. <h3>Patients or Participants</h3> N/A. <h3>Interventions</h3> Gene expression matrix of GSE141549 was downloaded from Gene Expression Omnibus (GEO) database and conducted to compare deep endometriosis with ovarian endometrioma. Differentially expressed genes (DEGs) were identified by limma package. Specific pathways related to OMA and DE were identified by gene set enrichment analysis (GSEA) and Weighted correlation network analysis (WGCNA). xCELL and CIBERSORT were used to analyze the difference in immune and stromal cell enrichment between OMA and DE. <h3>Measurements and Main Results</h3> 91 DE samples and 28 OMA samples were analyzed, from which we identified 406 DEGs between DE and OMA. WGCNA identified 14 co-expression modules, which were constructed by the top 5000 genes according to median absolute deviations. Module turquoise which was enriched in fibrosis and adhesion is most positively correlated with DE. Module blue, which was enriched in embryonic organ development and response to chemicals, is most positively correlated with OMA. The result of GSEA showed that cell adhesion-, fibrosis - and inflammation- related pathways were significantly enriched in DE samples, while pathways enriched in OMA related to steroid biosynthesis, metabolism of carbohydrates and amino acids. xCELL and CIBERSORT indicated that the differences between two groups were mainly in stromal cells rather than immune cells. <h3>Conclusion</h3> Through bioinformatic analysis, we explored the difference in gene expression profile between two common subtypes of endometriosis-OMA and DE. Fibrosis and inflammation seemed to be more associated with DE while OMA tended to be more related with steroid synthesis and metabolism. Further exploration of key genes and underling molecular mechanisms is needed to help developing novel therapeutic targets in treating endometriosis.