Fluorescence of the yellow fluorescent protein zFP538 strongly depends on concentration and starting pH from which pH profile is recorded. pH transitions typical for chromopeptides isolated from zFP538 can be observed for whole protein in diluted solutions. The quenching fluorescence of zFP538 is irreversible upon acidification or alkalization of the low concentrated solutions. In concentrated solutions, according to the data of dynamic light scattering, the protein zFP538 is strongly aggregated (or oligomerized) and become more stable against acid denaturation. Spectral changes on pH are almost reversible both for fluorescence and absorbance. Two major chromopeptides obtained from zFP538 have different spectral properties and no similarity to the spectral properties of the chromopeptide obtained from GFP.