The constraints exerted on the molecular edifices by different environmental parameters are not the same, which is translated by different adaptive strategies. Thus, for the extracellular and periplasmic enzymes of marine organisms that are directly exposed to environments in which large variations in temperature and salinity can occur, it is not an easy task to separate the adaptation of the enzyme to one of the two environmental parameters without the involvement of the other. In such a scenario, a comparative study of a marine psychrophilic and an estuarine mesophilic endonuclease I was undertaken. The different salt optima of the enzymes were taken into consideration when the temperature-dependent enzymatic properties were characterized. But the results did not show an adaptive strategy at the molecular edifice. For that purpose, we employed multiple all-atom explicit solvent and ions molecular dynamics simulations, in conjunction with the different temperatures at the nanosecond time scale, to analyze the structural flexibility of the cold-adapted enzyme, the VsEndA, and its mesophile homologous, the VcEndA. The Root Mean Square Fluctuation (RMSF) profiles of the two enzymes are almost similar with the most flexible residues located at loop regions, for both enzymes. We underlined a different trend against temperature for the two enzymes. The cold-adapted enzyme was dominated by the lowest temperatures; T=300 and T=318K, compared to its warm adapted homologous for which the highest temperature studied, T=326K is the dominant one. The lifetimes of the hydrogen bonding network of most flexible residues of both enzymes correlate well with the RMSF of the considered enzymes.