Aquatic origin collagen (Aqua-collagen) has been pursued as an alternative to mammalian origins. Acid-soluble collagen (ASC) and pepsin-soluble collagen (PSC) were successfully extracted from the skin of tilapia with the yield about 19-20% (basis of lyophilized dry weight), and examined for their physico-functional and structural properties. Both ASC and PSC containing at, a2 chains were characterized to be type I collagen and had lower denaturation temperature compared to mammalian origins. PSC (low telopeptides collagen) was selected for biomedical scaffolds construction due to its low immunogenicity. SEM analysis of fish collagen scaffolds showed a wide range of pore size distribution, high porosity, and high surface area-to-volume ratios. The tilapia collagen microfiber matrix scaffolds were grafted beneath the dorsal skin in 96 mice towards tissue regeneration, with bovine collagen microfiber matrix scaffolds (Avitene" UltraFoamn" sponge) serving as control. Biocompatibility evaluation in the dorsal tissue showed that implanted scaffolds degraded completely after 20 days with no pathological inflammatory tissue responses. These findings indicated that aqua-collagens microfiber matrix scaffolds were highly biocompatible in nature, exploring its feasibility for the development of scaffolds in tissue engineering.