Objective · To investigate the gene expression profiles of CD169+ and CD169- red pulp macrophages based on the expression of CD169 in murine splenic red pulp macrophages. Methods · The expression of CD169 in splenic red pulp macrophages in C57BL/6 wild-type (WT) mice was analyzed by flow cytometry and immunofluorescence. CD169 knockout (KO) mice were used as negative control. F4/80+ splenic red pulp macrophages were enriched and separated into CD169+ and CD169- subtypes. RNA-sequencing was performed on the two subtypes. DESeq2 was used to analyze differentially expressed genes at P<0.05 & |log2FC|≥1. Kyoto Encyclopedia of Genes (KEGG) enrichment analysis was used to classify the differentially expressed genes according to the pathways involved or functions they performed, and some differentially expressed genes were verified by quantitative real-time PCR (qPCR). Results · Expression of CD169 in some red pulp macrophages was confirmed by flow cytometry and immunofluorescence. There were 485 differentially expressed genes in CD169+ and CD169- subtypes. Some differentially expressed genes related to inflammation were highly expressed in the CD169- subtype. Conclusion · The CD169+ and CD169- red pulp macrophages have different transcriptional profiles, and CD169- red pulp macrophages have more features of M1 macrophages.