Macrophage is an essential component of the innate immune system. However， Streptococcus agalactiae has the ability to survive within macrophage， allowing it to infiltrate the central nervous system. To elucidate the mechanisms underlying the survival of S. agalactiae within macrophages， we investigated the genome-wide transcriptional changes of S. agalactiae following phagocytosis by RAW264.7 and explored the metabolic pathways and genes associated with the intracellular survival of S. agalactiae. The S. agalactiae strain HN016 was co-incubated with RAW264.7 and the intracellular bacteria were subjected to transcriptome sequencing （RNA-seq）， gene ontology （GO）， and Kyoto encyclopedia of genes and genomes （KEGG） enrichment analysis. Additionlly， HN016 was incubated with primary tilapia macrophages in vitro and RNA from the intracellular bacteria were extracted. Quantitative real-time PCR （qPCR） was used to verify the expression of the target genes. The results showed that a total of 1 215 differentially expressed genes （DEGs）， including 869 up-regulated genes and 319 down-regulated genes， were screened， compared with the untreated group. DEGs were significantly enriched in all three Go terms： molecular function， biological process， and cellular component. KEGG enrichment analysis showed that the main enriched pathways were ABC transporter， ribosome， quorum sensing， and glycolysis/gluconeogenesis. Among the DEGs， 27 virulence-related genes were screened， including fbsA （+8.65）， sip （+6.28）， cylD （+4.93）， and cfb （-4.65）. qPCR was used to validate the RNA-seq results， and the agreement between two datasets demonstrated the reliability of the RNA-seq analysis. The transcript levels of surviving bacteria in primary macrophages of tilapia were similar to those in mouse macrophages. Based on these findings， it was hypothesized that the noxious environment within macrophage enhanced the signaling mechanisms， energy transport capacity， and metabolic capacity of secondary metabolites produced by macrophages， as well as the expression levels of virulence-related genes of S. agalactiae.