Biosorption of extracellular polymeric substances (EPS) from Synechocystis sp. (cyanobacterium) with Cu(II) was investigated using fluorescence spectroscopy. Three fluorescence peaks were found in the excitation-emission matrix (EEM) fluorescence spectra of EPS. Fluorescence of peak A (Ex/Em = 275/452 nm) and peak C (Ex/Em = 350/452 nm) were originated from humic-like substances and fluorescence of peak B (Ex/ Em = 275/338 nm) was attributed to protein-like substances. Fluorescence of peaks A, B, and C could be quenched by Cu(II). The effective quenching constants (lg Ka) were 2.8–5.84 for peak A, 6.4–9.24 for peak B, and 3.48–6.68 for peak C, respectively. The values of lg Ka showed a decreasing trend with increasing temperature, indicating that the quenching processes were static in nature. The binding constants (lg Kb) followed the order of peak A > peak B > peak C, implying that the humic-like substances in EPS have greater Cu(II) binding capacity than the protein-like substances. The binding site number, n, in EPS-Cu(II) complexes for peaks A, B, and C was less than 1. This suggests the negative cooperativity between multiple binding sites and the presence of more than one Cu binding site.