Milkfish (Chanos chanos Forsskal.) is a euryhaline fish and an economically important species that inhabits marine coastal waters or fresh and brackish waters in the Asia-Pacific region. In the past, most of the studies in milkfish focused on the species’ propagation, nutrition, feed development, pathology, and culture while little attention has only been given to the immunology of the species. Lectins, a class of molecular-pattern recognition proteins called lectins which are present in viruses, prokaryotes and eukaryotes is being investigated in milkfish. These carbohydrate-binding proteins in invertebrates and vertebrates have been demonstrated as an important component of disease resistance in the innate immune system. This study aimed to sequence the milkfish liver transcriptome, annotate lectin genes and analyze the expression of the lectin genes.