•Scarb2c was more closely related to other vertebrate’s scarb2, while scarb2a may harbor new function in teleost.•Onscarb2a and Onscarb2c were more sensitive to A. hydrophilain liver while S. agalactiaein head kidney.•Onscarb2a and Onscarb2c might play important roles in the innate immune responses to bacterial invasion in Nile tilapia.