Background: Shipworms are voracious consumers of wood in marine environments. The animal burrows into both dead and living trees and secretes lignocellulosic enzymes that degrade lignocellulose. The degradation of these compounds by enzymes from different species of animals can be manipulated in biofuel production. Bactronophorus thoracites, which are believed to be endemic to Southeast Asia, have the potential to harbor novel lignocellulase enzymes.Results: Transcriptome data from the digestive gland and gill tissues was derived from RNA sequencing analysis. The analysis showed that both tissues revealed a potential gene associated with the breakdown of lignocellulose. The genes encode glycoside hydrolases (GHs), carbohydrate esterases (CEs) and other carbohydrate-active enzymes (CAZymes). Differential expression analysis demonstrated a different expression profile between both tissues. The digestive gland has showed to have several GH family members being upregulated, suggesting its main function in the degradation of plant-derived carbohydrates. The presence of enzymes associated in the breakdown cellulose and hemicellulose has been validated through CAZy annotation. A qPCR was performed on selected genes to confirm the RNA-seq findings and confirm the differential expression patterns. The evolutionary origin for two members of Glycoside Hydrolase 9 and one member of Glycoside Hydrolase Family 10, is distinctly separate compared to those from Teredinibacter turnarae, as revealed by the phylogenetic analysis. As previously reported, T. turnerae is exclusively localized in the gills, therefore, the presence and expression of these glycoside hydrolases in the digestive gland may indicate an alternative or supplementary digestive strategy in B. thoracites.Conclusion: The study demonstrates that both the digestive glands and gills displaying a distinct functional differentiation, with both tissues exhibits a high occurrence of enzymes catalyses in the hydrolysis of carbohydrates. The digestive glands seem to be harboured by mainly the enzymes for host-mediated carbohydrate degradation, while the gills are likely occupied by the symbiont-assisted carbohydrates degradation. The exclusive occurrence of AA genes in the gills, mainly associated with microbial oxidative enzymes such as lytic polysaccahraide monooxygenase (LPMOs), and together with phylogenetic analysis further support the explanation, displaying the distinct functional labour between the tissues.