Abstract: In this study,pepsin soluble collagen(PSC)was extracted from the skin of cod(Gadus macrocephalus)and tilapia(Oreochromis niloticus). And the molecular structure,thermal stability and peptide sequence in digest mixtures were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis,Fourier transform infrared spectra,X-ray diffraction,amino acid composition analysis,rotary viscometer and high-performance liquid chromatography-tandem mass spectrometry. The results showed that collagens from two different sources were in accordance with the typical type Ⅰ collagen and had similar secondary structure and tertiary structure,but the amino acid composition were different. The proline hydroxylation rate of O-PSC(49.1%)was higher than that of G-PSC(33.3%). The thermal denaturation temperature of O-PSC(24.7 ℃)was higher than that of G-PSC(13.8 ℃),the thermal stability was closely related to the proline hydroxylation rate. After two kinds of collagen were treated with the same enzyme,the characteristic peptides could be detected and identified. Conclusion:Different types of collagen had similar structure,but the different peptide fragments would be produced after the same enzymatic hydrolysis,which could be used to identify the source of collagen and provided a basis for the establishment of rapid analysis.