B‐cell lymphoma‐6 (Bcl6) is a transcriptional repressor that plays important roles in various physiological activities such as innate and adaptive immune response, lymphocyte differentiation, and cell cycle regulation in mammals. Two homologs of Bcl6a, namely Bcl6aa and Bcl6ab, are identified in teleost fish including medaka Oryzias latipes. The expression profiles of bcl6aa and bcl6ab in medaka were studied using reverse‐transcription polymerase chain reaction and in situ hybridization. The transcripts of bcl6aa and bcl6ab were detected from very early embryos such as the four‐cell stage until hatching. Bcl6aa and bcl6ab were clearly detected in the embryonic body from 5 days postfertilization onward by in situ hybridization. Bcl6aa was specifically expressed in the retina, whereas bcl6ab was expressed in entire embryonic body. The results referred to that both bcl6aa and bcl6ab originate maternally in the zygotes and may play major roles in embryogenesis of medaka. The transcripts of bcl6aa and bcl6ab were detected in all examined adult tissues, including immune organs such as the gill, spleen, kidney, liver, and intestine. The expression of bcl6aa and bcl6ab in the liver, spleen, head–kidney, and intestine could be upregulated or downregulated by lipopolysaccharide and polyriboinosinic–polyribocytidylic acid. These results indicate that both bcl6aa and bcl6ab may be involved in immune response in medaka. Bcl6aa and bcl6ab is duplicated homologs of BCL6 in fish. Medaka bcl6aa is located in the chromosome 4, bcl6ab is located in the chromosome 17. Bcl6aa & bcl6ab exist everywhere in adult tissues. Bcl6aa & bcl6ab are maternal origin and can be detected in very early embryos such as four‐cell stage, and are primarily detected in the yolk. From 5 dpf, bcl6aa is expressed in the eye only, whereas bcl6ab is expressed in the whole embryonic body. After stimulation by intraperitoneal injection of lipopolysaccharide and polyriboinosinic–polyribocytidylic acid, the expression level of bcl6aa and bcl6ab can be increased or decreased in the immune organs such as liver or spleen.