Abstract Acid-soluble collagen (ASC) and pepsin-soluble collagen (PSC) from the skin byproducts of paddlefish (ASC-P and PSC-P) and globefish (ASC-G and PSC-G) were purified and characterized. The imino acid contents of ASC-P, PSC-P, ASC-G and PSC-G were 194.1, 197.9, 186.4 and 189.7 residues/1000 residues, respectively. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared spectroscopy (FTIR) confirmed that all four samples composed of two different α1- and α2-chains with integrated triple-helical structure. Denaturation temperatures of ASC-P, PSC-P, ASC-G and PSC-G were 29.6, 28.2, 27.4 and 26.9 °C, respectively. Based on Transmission electron microscopy (TEM) observation, all four samples could assemble into fibrils in vitro with D-periodicity. However, the fibril-forming rate of ASC-P and PSC-P was more rapid than that of ASC-G and PSC-G. Scanning electron microscopy (SEM) analysis confirmed well-defined fibril morphologies,the diameter of fibrils from ASC-P and PSC-P was thicker than those of ASC-G and PSC-G after 24 h incubation. These results indicated that paddlefish and globefish skin collagens could be alternatives to terrestrial collagens for applications in food-packaging, nutraceutical and pharmaceutical industries.