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Atlantic bonito meat has economic potential as an alternative to mackerel consumption. Thus, considering the presence of myoglobin (Mb) in red fish muscles, we report the characterisation of Atlantic bonito Mb compared to Atlantic and Tinker mackerel Mbs since this haemoprotein is implicated in lipid oxidation and fish meat preservation. A plethora of biochemical approaches were employed to purified Mb from Atlantic bonito and determine the autoxidation rate constant (0.189 ± 0.009 h−1), melting temperature (Tm = 72.84 ± 1.02 °C) and pseudoperoxidase activity in different conditions (pH and several cations). Atlantic and Tinker mackerel Mbs showed a lower Tm (∼66.85 °C), while oxyMb autoxidation rate constant was higher for Atlantic mackerel (∼1.08-fold) and lower for Tinker mackerel (∼1.35-fold) compared to Atlantic bonito. This Mb had a Michaelis-Menten constant (Km) of 38.63 ± 1.89 μM, ∼2.49-fold and 2.27-fold lower than Atlantic and Tinker mackerel Mbs, respectively. Atlantic bonito Mb primary structure has 146 amino acid residues with the N-terminal acetylated and 25 amino acid substitutions with respect to Atlantic and Tinker mackerel Mbs. In silicoanalysis revealed that 7 out of 25 substitutions are close to the haem-pocket, while 18 out of 25 are far from this region. All substitutions, except H20, L70 and L81 are exposed on the protein globular surface. Overall, the results of this research provide new information for future studies that will be useful to the fish industry for preservation of frozen or canned Atlantic bonito meat considering the presence of Mb as a reactive haemoprotein.