The diversity of prokaryotic and eukaryotic phytoplankton was studied along a gradient of salinity in the solar salterns of Bras del Port in Santa Pola (Alacant, Spain) using different community descriptors. Chlorophyll a, HPLC pigment composition, flow cytometrically-determined picoplankton concentration, taxonomic composition of phytoplankton (based on optical microscopy) and genetic fingerprint patterns of 16S (cyanobacteria- and chloroplast-specific primers) and 18S rRNA genes were determined for samples from ponds with salinities ranging from 4% to 37%. Both morphological and genetical descriptors of taxonomic composition showed a good agreement and indicated a major discontinuity at salinities between 15% and 22%. The number of classes and the Shannon diversity index corresponding to the different descriptors showed a consistent decreasing trend with increasing salinity. The results indicate a selective effect of extremely high salinities on phytoplanktonic assemblages.