This paper is a retrospect of our research works on small molecular weight protease inhibitors and peptide toxins, all of them are active peptides. The Lysin active fragment of the double headed mung bean trypsin inhibitor has been intensively studied. The approaches of sequence determination, gene expression and mutagenesis as well as peptide synthesis are used to indicate that the essen- tial core of the inhibitor is composed of two conjugated disulfide loops each with nine-residues, which shares high homology with the cyclic peptide sun flower trypsin inhibitor. Another described inhibitor is the Trichosanthes trypsin inhibitor belonging to the squish family, its gene sequence was first reported in this family. The studied peptide toxins include scorpion toxins and conotoxins. Many novel potassium channel toxins were found from the scorpion Buthus martensi Karsch, in- cluding the calcium dependent BK or SK potassium channel toxins and voltage dependent toxins. Some of them have two deferent functions displaying at separated region, their structure-function relationships were elucidated. The expressed recombinant scorpion chloride toxin has a potential in treatment of malignant gliomas. From 16 species of cone snail 50 novel conotoxin peptides were identified, and 134 novel conotoxin genes were cloned. Three unreported superfamilies were characterized, designated as V, Y, K superfamily, respectively; some new disulfide frame and arrangement, unique motif, D-form residue in the toxin primary structures were found; the genomic structure of A superfamily was analysed, in the intro there is a very conserved sequence at the 3’end which could be used as a primer to clone more new conotoxin genes; the biological function of some conotoxins were elucidated.