In intertidal marine crustaceans, phenotypic variation in physiological and life-history traits is pervasive along latitudinal clines. However, organisms have complex phenotypes, and their traits do not vary independently but rather interact differentially between them, effect that is caused by genetic and/or environmental forces. We evaluated the geographic variation in phenotypic integration of three marine crab species that inhabit different vertical thermal microhabitats of the intertidal zone. We studied seven populations of each species along a latitudinal gradient that spans more than 3000 km of the Chilean coast. Specifically we measured nine physiological traits that are highly related to thermal physiology. Of the nine traits, we selected four that contributed significantly to the observed geographical variation among populations; this variation was then evaluated using mixed linear models and an integrative approach employing machine learning. The results indicate that patterns of physiological variation depend on species vertical microhabitat, which may be subject to chronic or acute environmental variation. The species that inhabit the high- intertidal sites (i.e., exposed to chronic variation) better tolerated thermal stress compared with populations that inhabit the lower intertidal. While those in the low-intertidal only face conditions of acute thermal variation, using to a greater extent the plasticity to face these events. Our main results reflect that (1) species that inhabit the high-intertidal maintain a greater integration between their physiological traits and present lower plasticity than those that inhabit the low-intertidal. (2) Inverse relationship that exists between phenotypic plasticity and phenotypic integration of the physiological traits identified, which could help optimize energy resources. In general, the study of multiple physiological traits provides a more accurate picture of how the thermal traits of organisms vary along temperature gradients especially when exposed to conditions close to tolerance limits.