Mysis diluviana, the opossum shrimp, is a key link between offshore benthic and pelagic foodwebs in the Laurentian Great Lakes. Nucleic acid and protein indices (RNA/DNA, DNA/protein, %protein, DNA/weight), which have been related to growth and protein synthesis rates, were assessed as measures of mysid condition. We examined autumn inter-annual and spatial patterns in these metrics in juvenile and adult female M. diluviana in Lake Ontario from 2001 to 2005. Males were not included because initial results of the present study indicated that larger, mature males entered a physiological decline in autumn. Nucleic acid/protein indices had a sufficient range and sensitivity to detect differences among years and habitats. In years when M. diluviana was in poor condition, nucleic acid and protein indices were similar to laboratory values of animals with low growth rates, values which were slightly above the nucleic acid and protein values of fasting animals. Mysids which were deemed to be in better condition in Lake Ontario had similar condition indices to those in Lake Huron. When differences existed, inshore mysids tended to be in poorer condition than offshore mysids, supporting the hypothesis that improved food resources may encourage offshore movement of mysids during the growing season. Zooplankton areal biomass, and female % total lipids and fecundity were not correlated with the nucleic acid and protein condition indices. However, key essential fatty acids and total saturated fatty acids had significant associations with nucleic acid and protein indices; this indicates that food quality is an important determinant of condition in M. diluviana.