Basic leucine zipper transcription factor ATF-like (BATF) -3 is a member of the activator protein 1 (AP‑1) family of transcription factors and is known to play a vital role in regulating differentiation of antigen-presenting cells in mammals. In this study, two BATF3 homologues (termed BATF3a and BATF3b) have been identified in rainbow trout (Oncorhynchus mykiss). Both genes were constitutively expressed in tissues, with particularly high levels of BATF3a in spleen, liver, pyloric caecae and head kidney. BATF3a was also more highly induced by PAMPs and cytokines in cultured cells, with type II IFN a particularly potent inducer. In rIL-4/13 pre-stimulated cells, the viral PAMPS polyI:C and R848 had the most pronounced effect on BATF3 expression. BATF3 expression could also be modulated in vivo, following infection with Yersinia ruckeri, a bacterial pathogen causing redmouth disease in salmonids, or with the rhabdovirus IHNV. The results suggest that BATF3 may be functionally conserved in regulating the differentiation and activation of immune cells in lower vertebrates and could be explored as a potential marker for comparative investigation of leucocyte lineage commitment across the vertebrate phyla.