Primary gypsum represents an excellent paleobiological archive due to its early and fast growth, favoring the preservation of delicate biomineralized structures. The Mediterranean region is renowned for evaporite deposits that formed during the Messinian salinity crisis (MSC), an event that supposedly annihilated most of the marine biota. However, the Messinian evaporites have been scarcely studied for their fossil content. Abundant nano-sized planktic diatoms and associated organic matter are observed for the first time in bottom-grown gypsum crystals that formed during the early stage of the MSC in different marginal basins of the western Mediterranean. This discovery increases our knowledge of the Messinian biota and reveals that nano-sized planktic diatoms played a prominent role in carbon and silicon export during gypsum deposition. The co-occurrence of these diatoms with larger diatoms, possibly associated with a deep chlorophyll maximum, suggests that Messinian gypsum formed in stratified and relatively deep basins (far below the photic zone), typified by marine conditions in the upper water column. The nano-sized planktic diatoms may have taken advantage of the hydrological reconfigurations experienced by the Mediterranean since the onset of the MSC. This study confirms that primary gypsum represents a promising archive of information for elucidating the marine biotic response to an ancient environmental crisis.