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The rheological behavior, gel properties and nanostructure of complex modified fish scales gelatin (FSG) by pectin and microbial transglutaminase (MTGase) were investigated. The findings suggested that MTGase and pectin have positive effect on the gelation point, melting point, apparent viscosity and gel properties of FSG. The highest values of gel strength and melting temperature could be observed at 0.8% (w/v) pectin. Nevertheless, at highest pectin concentration (1.6% w/v), the gel strength and melting temperature of complex modified gelatin gels decreased. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) analysis revealed that MTGase catalyzed cross-links among soluble fish scales gelatin - pectin complexes, which could be responsible for the observed increase in rheological behavior, gel strength and melting temperature of modified complex gels.