The lipocalin family of proteins functions in the transport of steroids, carotenoids, retinoids, and other small hydrophobic molecules. Recently, a lipocalin (MrLC) was isolated from the prawn Macrobrachium rosenbergii and its expression varied with the molting cycle. In this study, knockdown of the MrLC gene by RNA interference (RNAi) was performed and resulted in a shift in body color from blue to orangish red over the entire carapace. By immune-gold electron microscopy, MrLC was found to co-localize with the lipid droplets in subepidermal adiose tissue that were found to be decreased dramatically in MrLC knockdown prawns, in which a reduction in relative fat content was also quantified. Furthermore, MrLC was found to specifically bind astaxanthin and molt hormone (20-hydroxyecdysone) in both in vitro ligand binding assay and in vivo native ligand detection. These results suggested that MrLC plays roles in the regulation of coloration through its association with astaxanthin and may also be involved in the regulation of molting in crustacean.