Petrolisthes crabs inhabit a wide range of coastal environments, from the upper intertidal to the subtidal, experiencing regular changes in pH, salinity, and temperature. Hence, such subtidal and intertidal invertebrates are likely to show physiological and biochemical adaptive responses in order to successfully develop during early ontogenetic stages and thus reach reproduction. We herein evaluated the biochemical responses to contrasting environmental conditions of the early ontogenetic stages of two coastal crabs from the Southeast Pacific coast: Petrolisthes laevigatus and Allopetrolisthes punctatus. For this purpose, stage I embryos of both species were subjected to two treatments: (1) emersion (i.e., a daily 3 h aerial exposure until the zoeas hatched) and (2) immersion (i.e., uninterrupted underwater submersion until the zoeas hatched); the total contents of glucose, proteins, lipids, and fatty acids of the organisms were measured in stage I embryos and recently hatched zoeas in order to assess the biochemical constitution of the two species. Both species showed changes in their energetic reserves when treatments within species were compared. Our results found that A. punctatus was negatively affected by stressful periods of emersion, while P. laevigatus showed the opposite tendency and was affected by periods of immersion. The sensitivity of the response and the contrasting outcomes for these two crabs underpin the fact that changes in environmental conditions along the Chilean coast due to climate change (e.g., increased anoxic coastal waters) may have significantly negative consequences on the populations of these ecologically important species and the associated taxa within their ecosystems.