Affinity chromatography is one of the most powerful techniques in selective purification and isolation of a great number of compounds. Affinity ligand is the most important factor in affinity chromatography, therefore, the selection and the screening of affinity ligand become the first issue to be considered when a novel type of affinity packing or a novel system of affinity chromatography needs to be developed. In combination with the research work of the author' s group, this paper briefly summaries the recent progresses in selection, screening and application of affinity ligands. A new screening method with antisense peptide based combinatorial peptide libraries has been developed to search the affinity ligands for target proteins and peptides. This strategy is simpler and more effective than the conventional combinatorial strategy. The work including syntheses and screening is greatly reduced and the structural determination of the ligands becomes easy by using this method. Furthermore, the new method has been successfully applied to the screening of inhibitors for influenza A virus and SARS coronavirus, as well as the construction of quartz crystal microbalance ( QCM) biosensor for human interferon-beta.