Water samples were collected from four different salt concentrations at a solar saltern in Puglia, Italy.  The DNA was extracted from cell pellets of each sample and used to study the microbial diversity with a fingerprinting technique using LH-PCR and Bacteria and Archaea specific primers.  Additionally, the samples were plated onto 16 different media for the isolation of the bacteria, and initially 140 isolates were obtained from different plates.  Of these, 64 isolates were subjected to polyphasic taxonomy.  This included gram stains, lipid analysis, antibiotic resistance, carbon and nitrogen utilization, and 16S rRNA gene sequences among other tests. The data from the rDNA gene sequencing were analyzed using the Ribosomal Data Base Project (RDB II - version 9).  Other polyphasic taxonomic data were analyzed based on the data in Bergey’s Manual.  Most of the time the two procedures agreed but there were several instances when the Phylotype data was in conflict with the Phenotypic data.  For example, the 16S rDNA identifying an organism as a member of the genus Bacillus when it was gram negative, did not form spores, and was killed by heating.  Possible explanations for such discrepancies will be discussed.