In the present study, we investigated to find novel ligands for low molecular weight environmental toxin, microcystin-LR (MC-LR) by using phage display technology. Two random libraries, displaying linear 12-mer peptides and cyclic 7-mer peptides, were screened against the immobilized target respectively. After three rounds of panning, phage clones that recognized microcystin-LR specifically were obtained from both the linear and the constrained libraries, proved by enzyme-linked immumosorbent assays and immunoprecipitation assays. DNA sequencing indicated that peptides displayed on some of the selected clones shared consensus sequences. Compared with traditional methods, this approach provided a cheaper and more rapid alternative to screen specific ligands for microcystin-LR. Moreover, since it is rather difficult to take small molecules as targets of phage display libraries, the success of this experiment expanded the applications of phage display technology, and provided a new avenue to study environmental small molecular toxins.