The brown shrimp Crangon crangon shows high reproduction rates, feeds opportunistically on endo- and epibenthic organisms and is apparently well adapted to variable environmental conditions. Previous electrophoretic studies revealed a high level of polymorphism and no consistent phenotype of digestive enzymes between individuals. In order to understand the biological reason of digestive enzymes polymorphism and underlying biochemical processes, we performed a transcriptome-based study of digestive enzymes of C. crangon. Detailed sequence analyses of triacylglycerol lipase, phospholipase A2, alpha-amylase, chitinase, trypsin and cathepsin L were performed to identify putative isoforms. The number of isoforms varied among enzymes: for lipases, phospholipase A2 showed a higher number of isoforms than triacylglycerol lipase, while carbohydrase chitinase showed a higher number of isoforms in comparison with alpha amylase. Furthermore, cysteine proteinases showed a lower polymorphism than serine proteinases. We propose that the expression of polymorphic digestive enzymes indicates high plasticity in food utilization by the brown shrimp. Alternative splicing may be the driving force of the heterogeneous patterns of digestive enzymes in C. crangon.