Marine collagen is gaining more attraction than terrestrial collagen because it is free of zoonotic disease and religious constrain. In this study, we aimed to investigate and compare the physicochemical properties and functional characteristics of acid-soluble collagen (ASC-MF) and pepsin-soluble collagen (PSC-MF) extracted from scales of Megalonibea fusca. ASC-MF and PSC-MF were evaluated in terms of yield, collagen type, amino acid composition, thermal stability, microstructure, cytotoxicity, and other physicochemical parameters. ASC-MF and PSC-MF depicted 1.72 ± 0.2% and 11.72 ± 0.3% of dry weight yields, respectively, and were identified as type I collagen with an intact triple-helical structure by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), spectroscopic analysis, and electron microscopy. Additionally, compared with many temperate and tropical species, ASC-MF and PSC-MF showed higher thermal stability, with the maximum transition temperature (T