The aim of this study was to compare seasonal variations in the metabolism of two crayfish species with different habitats, Parastacus defossus that lives in subterranean galleries with low oxygen concentrations and Parastacus brasiliensis that lives in oxygenated environments. The metabolism of the species was compared, mainly evaluating the mobilization of the reserves for the reproductive period, and the metabolic response during the seasonal cycle. Seasonal sampling was conducted from spring 2006 to winter 2007. P. brasiliensis was collected at Mariana Pimentel, and P. defossus at Lami, Porto Alegre, Rio Grande do Sul. Hemolymph, hepatopancreas, muscle, gills, and gonads were removed for determination of glucose, free glucose, glycogen, lactate, total protein, total lipids, total cholesterol, and arginine phosphate. The hepatopancreatic and gonadosomatic indexes were determined. The results showed different seasonal responses between the species for all metabolic parameters, with the exception of proteins in gills, and of lactate in haemolymph. Lactate levels were slightly, but insignificantly, higher in P. defossus than in P. brasiliensis during the period of reduced oxygen. A significant difference between sexes was recorded in only some metabolites. The variability of the metabolism appears to be related to the reproductive period, but the exploratory activity in the environment also seems to be related to these variations. However, other factors may also be influencing the metabolism, such as the availability of food, and environmental conditions such as water, pH, temperature and dissolved oxygen levels, as previously observed for other decapods.