Background:　The　molecular　basis　for　the　disparities　between　primary　ovarian　cancer　(POC)　and　ovarian　cancer　secondary　to　breast　cancer　(OCSTBC)　remains　poorly　understood.　This　study　aimed　to　explore　the　different　characteristics　between　them　through　genomic　analysis.　Methods:　We　performed　differentially　expressed　genes　(DEGs)　analysis　between　POC　(n=96)　and　OCSTBC　(n=44)　groups　with　transcriptome　data　and　revealed　the　enriched　biological　pathways　with　Kyoto　Encyclopedia　of　Genes　and　Genomes　(KEGG)　and　Hallmark　gene　sets　between　these　two　groups.　Then,　the　Microenvironment　Cell　Populations　(MCP)-counter　and　Cell-type　Identification　by　Estimating　Relative　Subsets　of　RNA　Transcript　(CIBERSORT)　algorithms　were　applied　to　evaluate　the　immune　infiltration　in　tumor　microenvironment　(TME)　between　them.　Finally,　we　performed　the　association　analysis　within　single　nucleotide　polymorphism　(SNP)　data　and　obtained　some　meaningful　SNPs　and　candidate　genes　for　further　transcriptomic　analysis.　Results:　We　identified　a　total　of　13　cancer-related　genes　including　GATA3,　FOXA1,　CCND1,　and　TTK　between　POC　(n=96)　and　OCSTBC　(n=44)　groups　with　DEGs　analysis.　Integrated　analysis　revealed　more　significant　immune-enriched　pathways　in　the　POC　than　in　the　OCSTBC　group.　Most　immune　cells　had　higher　infiltration　abundance　in　POC,　except　M2　macrophages,　which　was　higher　in　OCSTBC.　In　SNP　analysis,　four　SNP　regions　(8q12.1,　11q21,　11q24.3,　and　17q25.3)　were　found　to　be　significantly　correlated　with　phenotypes　(POC/OCSTBC),　and　importantly,　some　new　susceptibility　genes　such　as　ETS1,　CWC15,　and　XKR4　were　revealed　to　potentially　be　associated　with　distinction　between　POC　and　OCSTBC.　Conclusions:　Our　study　provides　a　systematic　molecular　characteristic　between　POC　and　OCSTBC　and　suggests　a　pressing　need　to　develop　some　specific　therapeutic　strategies　in　certain　types　of　ovarian　cancer.　©　AME　Publishing　Company.