Molecular dynamics calculations of pressure effects on mStrawberry and mCherry fluorescent proteins are reported. The simulations reveal that mStrawberry has much floppier structure at atmospheric pressure, as evidenced by larger backbone fluctuations and the coexistence of two conformers that differ by Ser146 orientation. Consequently, pressure increase has a larger effect on mStrawberry, making its structure more rigid and reducing the population of one of the conformers. The most significant effect of pressure increase is in the hydrogen-bonding network between the chromophore and the nearby residues. The quantum-mechanics/molecular mechanics calculations of excitation energies in mStrawberry explain the observed blue shift and identify Lys70 as the residue that has the most pronounced effect on the spectra. The results suggest that pressure increase causes an initial increase of fluorescence yield only for relatively floppy fluorescent proteins, whereas the fluorescent proteins that have more rigid structures have quantum yields close to their maximum. The results suggest that a low quantum yield in fluorescent proteins is dynamic in nature and depends on the range of thermal motions of the chromophore and fluctuations in the H-bonding network rather than on their average structure.