In view of the relationship between shifts in diet composition and the activity of digestive enzymes in penaeid shrimp, the present study focused on the analysis of digestive trypsin and α-amylase activities of wild Farfantepenaeus duorarum (Burkenroad, 1939) juveniles and their changes in phenotypic expression, during the molt cycle as endogenous factor and their changes due to different feeding regimes (exogenous factor) in relation with δ¹³C and δ¹⁵N isotopic signature as an index of food assimilation induced by the seasonal availability of food items in the nursery area. Wild juveniles of F. duorarum were captured from April 2007 to February 2008, in the Celestun coastal lagoon, Yucatan, Mexico. Samplings were carried out considering all quarters of the lunar cycle and in each of the recognized seasons for this region: dry, rainy, and the Nortes (North Wind). Copepods and amphipods were the main source of food for juveniles of F. duorarum. Values of δ¹³C in the muscular tissue were near -20‰ hence the feeding regime of F. duorarum in the lagoon was composed by material of marine origin. Isotopic signature differences were found between the three annual seasons. It is an opportunist generalist organism that is located in the 4^th trophic level. The digestive enzymatic activities of both trypsin and α-amylase in fresh hepatopancreas tissue showed an interaction between season and molt stages (p < 0.05). Activity of the trypsin was highest during the Nortes at molt stage C (140 mU mg^-1 HP) and activity of α-amylase was higher in the Nortes at stage B2 (674 mU mg^-1 HP). The amylase/trypsin ratio also showed significant interaction between season and molt stages (p < 0.05), with higher values in premolt stages during the rainy and Nortes seasons. Isoforms of these digestive enzymes differed in expression according to the molt stage and also to the season with expression generally being greater at stage C.