Lipid quality was evaluated in Montastrea spp. under sediment- and heat-stressed conditions. Levels of total lipid in M. annularis subject to experimental sedimentation were highly variable (10.07 - 210.37 mg lipid/g dry tissue) and did not differ significantly with treatment (p > 0.25). The ratio of storage lipid (wax ester + triacylglyceride) to structural lipid (sterol esters + phospholipid) decreased significantly (from 0.25 to 0.14, n = 22, p < 0.01) in treatment colonies. Fatty acid methyl esterization (FAME) analysis of colonies exposed to experimental sedimentation showed a reduction of the algal, 18:3(n-6) and 18:4(n-3), polyunsaturated fatty acid (PUFA) in the polar fraction of tissue lipid extracts. This loss of PUFA suggests a loss of algal membrane in sediment-stressed colonies. Lipid quality was similarly measured in 20 colonies of M. faveolata over a 10-day period. Mean (n=20) ratio of storage to structural lipid in M. faveolata dropped from 2.43 to a level of 0.98 (p < 0.01) immediately following a natural sedimentation event before recovering to levels of 1.4 and 2.9 post-storm days 2 and 4, respectively. A sensitivity analysis of lipid content with decreasing tissue sample size was conducted and stress experiments were repeated in M. annularis using Vacutainer® blood collection tubes to collect microtissue (3-5 polyps) samples without destroying skeleton of the sample colonies. A significant decrease in storage:structural lipid ratio (from 0.91 to 0.31, p < 0.01) in sediment stressed colonies was also detected using the microtissue technique. Colonies of M. annularis subject to heat-stress (35oC) exhibited no significant change in storage lipid ratio, while levels of Free Fatty Acids (FFA) increased significantly from 0.012 to 0.156 mg lipid/g dry tissue (n = 22, p < 0.05). FAME analysis of tissue lipids extracted from the heat-stressed colonies showed changes in the polar fraction, with significant decreases in the 18:3(n-6), 18:3(n-3), 18:4(n-3), 20:4(n-6) and 20:5(n-3) (p < 0.05) PUFA and subsequent significant increases in the saturated fatty acids, 16:0 and 18:0 (p < 0.05). Changes in lipid quantity and quality indicate possible oxidation and preferential digestion of zooxanthellar membranes in M. annularis subject to severe heat stress. The results of this study suggest that the relative abundance of lipid subclass components can indicate sub-lethal environmental stress in M. annularis and M. faveolata on short time scales. Results from the microtissue collection techniques are consistent with other forms of tissue analysis which require destruction of the coral colony. Furthermore, micro-tissue collection techniques permit repeated monitoring coral colonies to detect the manifestation of stress from first impact (hours/days) at the cellular level before these effects become visually apparent. This technique may be a viable method to study how individual, colony-level response to environmental stress is manifest in community structure over longer time scales (years/decades).