Gelling behaviors of partially purified myofibrillar proteins (PPMP) extracted from Indian mackerel (IM) and threadfin bream (TB) as a function of heating temperatures (20–75°C) were comparatively studied. PPMP obtained from IM (IM‐MP) showed lower turbidity and surface hydrophobicity as compared to those extracted from TB (TB‐MP). Moreover, lower disulfide bond content was noticed in IM‐MP (7.7–9.46 mol/106 g protein) as compared to TB‐MP (10.99‐13.95 mol/106 g protein) during the heating process. There was no major difference in the amino acid profile noticed between PPMP from both the species, except lysine and glutamine contents, which were higher in TB‐MP. Structural analysis, FTIR spectra, amide I band, and fluorescence intensity substantiated those changes. The protein pattern also revealed autolysis of IM‐MP. The transmission analysis also showed lower aggregation and crosslinking ability of IM‐MP than TB‐MP. Therefore, poorer gelling behavior of IM‐MP reconfirmed the inferior gel property of surimi gel from IM to gel from TB. Potential development is still required for the improvement of the gel properties of dark‐fleshed fish surimi such as IM.Practical ApplicationIndian mackerel (IM) is an abundant and widely captured fish species. Due to overexploitation of lean fish, pelagic fish could be explored as a potential raw material for surimi production. However, poor gelling properties of IM limit its use in the surimi industry. This study provides an insight into the gelling behavior of myofibrillar proteins from IM during the gelation process in comparison with the lean fish (threadfin bream). Overall, structural and rheological changes of myofibrillar proteins play a role in gelation, thus affecting gel properties between two species. Further improvement of the gel of IM is still required.