CD36 is a transmembrane glycoprotein belonging to the scavenger receptor class B family which plays crucial roles in innate immunity. Although CD36 is widely documented in mammals, the study of its functions in fish is still limited. Here we report the identification of a zebrafish cd36 homologue. Zebrafish cd36 has a higher gene expression in the tissues of intestine and liver but very low in kidney and swim bladder. We find cd36 mRNA is maternally expressed and is mainly restricted to the intestine, branchial arches and regions around the lips after the segmentation stage during embryogenesis. Functionally, the recombinant Cd36 corresponding to the large extracellular loop is capable of binding both the Gram-negative and Gram-positive bacteria. These results indicate that zebrafish Cd36 is a microbial-binding molecule. The study expands our knowledge of the function of scavenger receptor molecules in fish innate immune process.