In this study, we selected and validated six widely used endogenous genes (i.e., 18SrRNA, ACTB, TUBA, UBCE, GAPDH and EF1A) in the studies of gene expression and mRNA transcription level with the qPCR method, to find that these reference genes all exhibited different variabilities to some extent during the different periods of vaccination and infection in tilapia. Here, GAPDH is linked to infection.