Aeromonas hydrophila causes serious economic losses to the black carp (Mylopharyngodon piceus) industry. In this study, we analyzed the spleen of disease-resistant and susceptible black carp by RNA-seq. Overall, a total of 5243 terms were enriched in the gene ontology (GO) analysis, and 323 related pathways were found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. A total of 1935 differentially expressed genes were found and were primarily involved in cell adhesion, pathogen recognition, cellular immunity, cytokines, complement systems, and iron transport. Sixteen of the differently expressed genes involved in the immune response and the accuracy of the transcriptome data were further validated by quantitative real-time PCR (qRT-PCR). We observed Tissue sections of the spleen infected with A. hydrophila and the control group and found that the spleen of the infected group had necrosis.