The Antarctic krill, Euphausia superba, and the Northern krill, Meganyctiphanes norvegica, are closely related species but occupy significantly different trophic and climatic environments. E. superba holds a key position as a phytoplankton grazer in the Southern Ocean. The omnivorous M. norvegica is an important member of plankton communities in the Northeast Atlantic. Both species expressed high proteolytic activities which were dominated by serine proteinases. In the stomachs of Antarctic krill, activities of total proteinase, trypsin, and chymotrypsin were significantly higher than in Northern krill. In the midgut glands, however, total proteinase and trypsin activities were similar in both species, but chymotrypsin activity was significantly higher in Antarctic krill. Moreover, Antarctic krill expressed four trypsin isoforms while only one isoform appeared in Northern krill. Chymotrypsin was present in either species as one single isoform. Antarctic krill adapted to the low and patchy distribution of food by elevated enzyme activities and the expression of trypsin isoforms with slightly different catalytic properties. Presumably, these enzymes facilitate in concerted action the efficient utilization of proteins from phytoplankton, the major food. Northern krill, in contrast, seems not to be equipped to face food limitation. It expresses a “simple” or “basic” set of digestive enzymes for utilizing abundant and easily digestible prey.