Family Lethrinidae (Sho´our fishes, Shaari fishes) is one of the key families in the Red Sea and Indian Ocean fisheries. Some of its species were recorded in the International Union for Conservation of Nature (IUCN) Red List of species as endangered. In order to develop simple genetic marker that aid their rapid identification, fin clips of four lethrinid species were collected from local fish markets in Hurghada city. These species were Lethrinus lentjan, L. harak, L. microdon, and L. mahsena. DNA was extracted from these samples and subjected to polymerase chain reaction (PCR) amplification for the mitochondrial 12S ribosomal RNA (rRNA) and the nuclear 5S rRNA genes. The 12S rRNA PCR amplicons were sequenced. GenBank comparison and phylogenetic analysis for the 12S rRNA gene sequences resulted in clear identification for the sampled species. Meanwhile, a simple, 2% agarose gel electrophoresis for the 5S rDNA ran in a low voltage for 2 hours resulted in variable intraspecific patterns. These patterns appeared as 3 PCR bands of approximately 500 base pair (bp) in length for L. lentjan; 2 PCR bands at 500 and 400 bp for L. harak; single PCR band at 500 bp for L. microdon; and 3 bands at about 750, 500, and 400 bp for L. mahsena. Band separation was clear enough. 5S rDNA exhibited an accurate, interspecific, and easy-to-use genetic marker for identification of different lethrinid species covered by the current study.