Restriction fragment length polymorphisms of 16S rRNA genes of representative strains of the actinomycete species (P-100-1 Saccharomonospora halophila, A-3-4 Nocardiopsis sp., A-1 Nocardiopsis halotolerance, P-7-2 Nocradiopsis sp. and Microbispora sp.) were determined following the isolation and genes amplification. 16S rDNAs were amplified with two primers; 5\'-TCACGGAGAGTTTGATCCTG-3\' and 5\'-AGAAAGGAGGTGATC-3\'. Actinomycete 16S rRNA genes were used with eight restriction endonucleases (EcoRI, StyI, AvaI, BanI, HindIII, NaeI, AsnI and BanII) to obtain restriction fragment length polymorphisms (RFLPs). The PCR/RFLP profiles of SrRNA genes indicated that the actinomycete isolates are polyphylogenetic when digested with BanI restriction endonuclease. Also, some actinomycete strains are monophylogenetic in nature, such as N. A-3-4 and S. P-100-1. PCR-RFLPs of SrDNA is an effective marker to differentiate between the actinomycete strains in a much more accuracy than do the morphological studies alone.