Abstract: Halophilic microorganisms present in the hypersaline environments of solar salterns present a potential source of industrial and biotechnological applications .The Rapid identification of these microorganisms which are accurate and cost effective is a necessity in applied microbiology. There have been several systems developed in the past few years for rapid microbial identification. In the present study, GC FAME( Gas chromatography- Fatty acid methyl esters) analysis and 16s rDNA sequencing were compared for identification of four halophilic bacteria. Four halophilic bacterial isolates obtained from solar saltern sediment were analyzed . The isolates were identified with 16srDNA sequencing as Virgibacillus pantothenticus, Bacillus atrophaeus, Corynebacterium diphtheria and ,Idiomarina Zobellii .However in FAME analysis , the RTBSA 6 library did not confirm any matches for Idiomarina Zobellii. Comparative analysis, indicated that the FAME analysis results correlates to genotypic sequencing results. However,a halophilic bacterial FAME library should be established to enhance the accurate , rapid and cost effective investigation of halophilic microorganisms.