Metabolic regulation, control of gene expression or the evolutionary origin of new proteins are examples of biochemical adaptations that allow organisms to survive within a wide spectrum of environmental conditions. The North Sea shrimp Crangon crangon has high reproduction rates. It is an opportunistic feeder and shows to be well adapted to heterogeneous and variable environmental conditions. Previous studies revealed unusual expression patterns and isoforms of digestive enzymes with a high variability between individuals and between seasons. Such a pronounced variability is not common in other decapod species. The unspecific feeding habits of C. crangon can be seen as an adaptation to a variable environment. This may be supported by the heterogeneity of digestive endopeptidases due to the variability of food sources. Previous studies showed protein polymorphism as a phase in molecular evolution. It represents the first step in the long‐lasting establishment of mutations within populations. The reasons for the unusual heterogeneity of digestive enzymes in C. crangon are not yet clear, but a better understanding of this phenomenon can help to explain the extraordinary performance of C. crangon in a highly variable environment. We obtained the transcriptome of midgut gland tissue from C. crangon, which we used as a basis for gene expression analyses. Additionally, the obtained sequences were analysed for isoforms of the key digestive enzymes. First results indicate that the expression of digestive enzymes in C. crangon follow a similar pattern as previously seen in enzyme activities. Cysteine proteinases seem to have more isoforms participating in the extracellular digestion than serine proteinases. This approach will help to better understand processes that modulate the unique expression pattern of digestive enzymes and biochemical strategies that allow this species to exist in a very variable environment.