The accurate identification and evolutionary variations of the Red Sea shrimp resources, in particular, are still under debate. This work was designed for testing the utility of the 16S rRNA gene system in inferencing evolutionary variations among some Red Sea shrimp species compared with some other shrimp species. A close relationship was calculated between Penaeus latisulcatus  and P. japonicus. The distance value between P.  semisulcatus and P.  monodon was lower than the distance value between P. semisulcatus and P. vannamei. The distance value between P. vannamei and P. monodon was lower than the distance value between P.  vannamei and M. monoceros. The molecular markers developed in this study provide clear evidence confirming that the M. monoceros was distantly related to the other evaluated Red Sea shrimp species. The utility of 16S ribosomal RNA gene fragment sequences is appeared to deliver clear phylogenetic relationships among the evaluated shrimp resources. The utilization of the developed molecular markers in the reconstruction of the relatedness among various shrimp taxa should be maximized in the future. This strategy will open up new avenues in understanding the evolution of the Red Sea shrimp species.