The impact of global change forces marine species to acclimatize and adapt to new environmental conditions. Some species already experience environments that represent a challenge due to rapid and partly drastic variations, such as the North Sea. The brown shrimp, Crangon crangon, inhabits the shallow coastal areas of the North Sea. Its high abundance and high reproduction rates make this species an important member of the coastal ecosystem and a valuable target for local fisheries. This shrimp is apparently well prepared to thrive in a highly variable environment. However, it is still unknown, how this species manages to cope with these environmental changes at the metabolic level. Until now it was difficult to obtain the transcriptome of a non-model organism like the brown shrimp. However, next-generation sequencing technologies allow performing inexpensive and rapid transcriptome analyses. Here we report about the first transcriptome of midgut gland tissue from C. crangon, which we used as a basis for seasonal gene expression analyses. The brown shrimp seems to have the capability to express specific digestive enzymes depending on different seasonal requirements. Furthermore, C. crangon exhibits an extraordinary enzyme polymorphism, which may suggest a process of molecular evolution. Assuming that polymorphic expression of digestive enzymes is an adaptation to variable environmental conditions, the pronounced enzyme polymorphism observed in C. crangon may reflect an acute adaptive process of an organism coping with a changing environment.