A tier III, essential fish habitat analysis was used to evaluate the biochemical condition of common mummichog Fundulus heteroclitus residing in two isolated tidal salt marshes, one a relatively undisturbed polyhaline site dominated by Spartina alterniflora and the other a meso-oligohaline site dominated by an invasive variety of Phragmites australis. Stable isotopes signatures of C, N, and S in whole tissue samples of F. heteroclitus were used to compare the trophic spectrum for this species in each marsh as a function of the dominant macrophytes present with additional contributions from phytoplankton and benthic microalgae. Allometry of wet mass and its components, water mass, lean protein mass and lipid mass in individual fish exhibited hyperallometric patterns; and average lipid mass fell within the range reported for most fundulids, including F. heteroclitus. Significant differences were also detected in the allocation of lipid classes to energy reserves in the form of triacylglycerols (TAG) and free fatty acids. These reserves, especially TAG, are critical for reproduction, migration, and overwintering survival in many taxa and were significantly lower in fish collected in the P. australis-dominated marsh. Relative to the relatively undisturbed Spartina-dominated site, we tentatively conclude that the P. australis-invaded marsh was an inferior habitat for F. heteroclitus.