BackgroundThis　study　aimed　to　analyze　the　biomarkers　that　may　reliably　indicate　rejection　or　tolerance　and　the　mechanism　that　underlie　the　induction　and　maintenance　of　liver　transplantation　(LT)　tolerance　related　to　immunosuppressant　or　mesenchymal　stem　cells　(MSCs).MethodsLT　models　of　Lewis-Lewis　and　F344-Lewis　rats　were　established.　Lewis-Lewis　rats　model　served　as　a　control　(Syn).　F344-Lewis　rats　were　treated　with　immunosuppressant　alone　(Allo+IS)　or　in　combination　with　MSCs　(Allo+IS+MSCs).　Intrahepatic　cell　composition　particularly　immune　cells　was　compared　between　the　groups　by　single-cell　sequencing.　Analysis　of　subclusters,　KEGG　pathway　analysis,　and　pseudotime　trajectory　analysis　were　performed　to　explore　the　potential　immunoregulatory　mechanisms　of　immunosuppressant　alone　or　combined　with　MSCs.ResultsImmunosuppressants　alone　or　combined　with　MSCs　increases　the　liver　tolerance,　to　a　certain　extent.　Single-cell　sequencing　identified　intrahepatic　cell　composition　signature,　including　cell　subpopulations　of　B　cells,　cholangiocytes,　endothelial　cells,　erythrocytes,　hepatic　stellate　cells,　hepatocytes,　mononuclear　phagocytes,　neutrophils,　T　cells,　and　plasmacytoid　dendritic　cells.　Immunosuppressant　particularly　its　combination　with　MSCs　altered　the　landscape　of　intrahepatic　cells　in　transplanted　livers,　as　well　as　gene　expression　patterns　in　immune　cells.　MSCs　may　be　included　in　the　differentiation　of　T　cells,　classical　monocytes,　and　non-classical　monocytes.ConclusionThese　findings　provided　novel　insights　for　better　understanding　the　heterogeneity　and　biological　functions　of　intrahepatic　immune　cells　after　LT　treated　by　IS　alone　or　in　combination　with　MSCs.　The　identified　markers　of　immune　cells　may　serve　as　the　immunotherapeutic　targets　for　MSC　treatment　of　liver　transplant　rejection.