The Atlantic blue crab, Callinectes sapidus, is an economically, ecologically, and recreationally valuable decapod crustacean that inhabits estuaries along the Atlantic and Gulf coasts of the United States. In their natural environment, blue crabs are exposed to many stressors including anthropogenic contaminants, viruses and bacteria. Bacterial infection results in the depression of oxygen uptake, and impairs normal metabolic function in a manner that has not yet been fully elucidated. Our laboratory is developing NMR-based metabolomic tools for environmental research to discover metabolomic biomarkers of stress in marine organisms. We have used NMR spectroscopy to compare the response of the crab metabolome to depression of aerobic metabolism by injection of the bacterium Vibrio campbellii, versus elevation of aerobic metabolism by treatment with 2,4-dinitrophenol (DNP), a known uncoupler of oxidative phosphorylation. The corresponding NMR spectral variations between treatments were evaluated using chemometric tools for pattern recognition and biomarker identification, including principal components analysis and partial least-squares analysis. Metabolic changes were identified in crab hemolymph 30 min after injection with V. campbellii and DNP. Glucose, considered a reliable indicator for biological stress in crustaceans, and lactate, a metabolite indicating anaerobic respiration, provided the largest variations in the metabolomes, respectively. While biological variability and/or tight regulation of the hemolymph masked subtle metabolic changes at individual time-points, metabolic trajectory analysis revealed clear differences between the two modes of oxidative stress, providing insight into the biochemical pathways involved.