The interleukin-1 receptor/toll-like receptor (IL-1R/TLR) superfamily signaling involves myeloid differentiation factor 88 (MyD88) that acts as an important adapter protein. A Japanese flounder (Paralichthys olivaceus) MyD88 (jfMyD88) cDNA and gene were cloned, and found to have lengths of 1.5 and 3.01 kb, respectively. The ORF encodes 285 amino acids that contain a death domain and a Toll/IL-1 receptor domain. The gene is composed of 5 exons and 4 introns. The jfMyD88 gene is highly expressed in organs involved in immune functions, including the gills, intestines, kidney, skin and spleen. Three days after a fish was infected with Edwardsiella tarda, staining with anti-jfMyD88 polyclonal antibody revealed an increased population of MyD88-positive cells in the kidney and spleen. These results imply that MyD88 has an important role in the innate immune system in Japanese flounder.