Homologous molecular probes were used to examine in vivo molecular chaperone and polyubiquitin gene expression patterns in the American lobster, Homarus americanus, an ectothermic marine crustacean. Following long-term laboratory acclimation to temperatures experienced during overintering in nature, juvenile lobsters failed to elicit the classical "heat-shock response'' when subjected to an acute 13°C thermal stress. Levels of mRNA coding for molecular chaperones (HSC70, HSP70, and HSP90) and polyubiquitin were not induced during thermal stress or recovery in cold-acclimated animals. These results contrasted with those for lobsters acclimated to ambient Pacific Ocean temperatures that experienced an acute stress over an equivalent thermal interval. Ambient-acclimated lobsters displayed significant inductions in the mRNA levels for both molecular chaperones and polyubiquitin. Hyper- and hypo-osmotic stress were found to significantly induce HSP90 and polyubiquitin mRNA levels in ambient-acclimated juvenile lobsters. Additionally, osmotic and thermal stress interactively altered HSP90 and polyubiquitin gene expression in animals that received both types of stress. Physiological changes over the molt cycle significantly affected gene expression in claw muscles undergoing atrophy in preparation for molting. Molecular chaperone and polyubiquitin mRNA levels differed significantly between premolt claw and abdominal muscle, which does not undergo atrophy during the premolt stages.