This study compared the carbon isotopic composition of individual amino acids from muscle tissue and shell organic matter inclusions in Crassostrea virginica collected along a salinity gradient in the Rookery Bay estuary, Florida. Theintent was to assess the extent to which environmental signals relating to spatial and temporal variation in carbon sources were recorded in the amino acids of these materials. There was a trend toward enrichment in δ13C in all amino acids moving seaward along the transect in both organic matter pools, consistent with diminishing influence of terrestrial (C3) production and increased contributions of marine production. The magnitude of this trend was identical for both tissue and shell organic matter, although the values for several constituents of the shell organic matter (aspartic and glutamic acids and glycine) were consistently depleted by approximately 3‰ relative to their equivalents in tissue samples. Other amino acids were directly comparable despite a 2‰ offset in bulk isotopic compositions. Sites were distinguishable from one another in both the tissue and shell organic matter data sets. Although samples were collected across an annual cycle to examine seasonal change, no seasonality was found. The results presented here demonstrate that compound-specific amino acid analysis of carbon isotopes is a useful tool in the analysis and interpretation of biomineral organic materials.