Abstract During the Late Miocene the Lorca Basin, which was an integrated part of the Betic Strait, underwent desiccation. The present investigation was completed to determine the response of the diatom flora to environmental changes before this event. Near the city of Lorca (Province of Murcia, SE Spain) the outcrop area around the Serrata ridge was studied and a stratigraphic section of 125 m has been measured and sampled (115 samples). The Serrata ridge is capped by a 25 m thick gypsum bed (Gypsum Member of the Serrata Formation). The profile below these gypsum layers comprises marl, sandstone, gypsum and partially laminated diatomite (Varied Member of the Serrata Formation). The frequency of radiolaria, siliceous sponge spicules, siticoflagellates, ebridians, diatoms and diatom species has been determined quantitatively. For the lower 87.5 m of the section, which contains sufficiently well preserved diatoms, an age of latest Miocene (6.6–5.3 Ma; Magnetic Epoch 6 and 5) can be assigned by the presence of the diatom species Asterolampra acutiloba and Nitzschia reinholdii , applying the stratigraphic ranges of the species used in the North and Equatorial Pacific and in the Atlantic. In total, 116 diatom species and species-groups have been identified. However, the number of species per sample varies only between 13 and 36 species (a minimum of 300 valves counted). This low diversity, together with a dominance of one species-group, Thalassionema nitzschioides (up to 80%), which tolerates considerable ecological changes (e.g. in salinity) indicate that environmental stress must have prevailed during the sedimentation of the Varied Member of the Serrata Formation. Abundance fluctuations of this species-group, as well as changes in the composition of the remaining diatom assemblage and decreases in abundances of the siliceous microfossil groups, reflect repeated periods of interruption of the still marine influenced deposits before the deposition of thick gypsum layers. Several repetitive changes are indicated, where each cycle is characterized by an increase in meroplanktonic species (e.g. Paralia sulcata , Actinoptychus senarius ) and by a contemporary decrease in the holoplanktonic species towards the top, suggesting progressive environmental stress and a shallowing of the basin. Five of these cycles are clearly distinguished characterizing the initial stages of the evaporitic desiccation event in the Lorca Basin. Benthic diatoms are present only in low abundances (2–4%) and show no correlation with these fluctuations.