Fatty acid desaturases exist in all living organisms and play important roles in many different biologic processes, such as fatty acid metabolism, lipid biosynthetic processes, and pheromone biosynthetic processes. Using the available silkworm genome sequence, we identified 14 candidate fatty acid desaturase genes. Eleven genes contain 3 conserved histidine cluster motifs and 4 transmembrane domains, but their N-terminal residues exhibit obvious diversity. Phylogenetic analysis revealed that there are 6 groups; Bmdesat1 and Bmdesat5-8 were clustered into group 2, which is involved in Δ11 desaturation activity, and Bmdesat3-4 were grouped in group 1, which is involved in Δ9 desaturation activity. Twelve of the 14 genes have expressed sequence tag evidence. Microarray data and reverse transcription polymerase chain reaction analysis demonstrated that Bmdesat3-4 and Bmdesat10 were expressed from the larval to moth stages and in multiple tissues on day 3 of 5th instar larvae. Bmdesat9, Bmdesat11, and Bmdesat14 were expressed during the pupal and late-embryonic stage, suggesting that they may take part in fatty acid metabolism to provide energy. These results provide some insights into the functions of individual fatty acid desaturases in silkworm.