Spatio-temporal variations of 8 trace metals in planktonic amphipods were studied from a highly productive tropical estuary, the Cochin backwaters.The mean trace metal accumulation and bioaccumulation factors in amphipods were in the order Fe>Zn > Mn > Cu > Ni > Cr > Pb > Cd and Fe > Zn > Mn > Cu > Cr > Ni > Cd > Pb respectively. ANOVA revealed that the spatial and seasonal variations of trace metal content in amphipods were statistically significant.Hierarchical cluster analysis (HCA) has grouped the sampling stations into two clusters based on the trace metal concentrations in amphipods of Cochin backwaters. Thehigh bioaccumulating factors (BAF) reported in this studyindicating great trace metal accumulating capacityof amphipods. Two groups of elements were produced from statistical analysis using Principal Component Analysis (PCA). First group included Fe, Ni, Zn, Cr, Pb, Cd and Cu while second contained Mn. All metals exhibited higher concentrations in amphipods than their background values, signifying anthropogenic pollution in estuary.