Evaporite sediments are known to have formed during the Messinian high salinity crisis that has been recognized in many Mediterranean areas. This event was however never identified on the Maltese Islands. In this study, a Sr isotopic characterization of gypsum, found as secondary minerals in the Oligocene-Miocene formations of Malta and Gozo is performed. The 87Sr/86Sr values are discussed on the basis of comparison with the surrounding rock Sr isotopic signature. The data outline two distinguishable 87Sr/86Sr ratios for gypsum according to their facies. Most of crack-infilling mineral data suggest a downward fluid circulation in the Miocene sediment associated with interaction in the currently outcropping limestones. Some gypsum crystals found as crystallized spherules show significantly lower 87Sr/86Sr ratios, close to those defined in the literature for Messinian evaporate sediments. Taken together, this may suggest that an evaporate formation of Messinian age had in the past covered the present-day sedimentary sequence in Malta and Gozo.