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Over the last few years, pathogenic genes of TssT-1 toxin, MRSA and VRSA have increased. Therefore, the identification of staphylococcal species in Basrah city using 16SrRNA gene nucleotide sequencing has revealed the following species: S.aureus, S.epidermidis, S.haemolyticus, S.gallinarum, S.hominis, S.xylosus and S.arlettae. Rooted NJ tree showed that S.epidermidis is the root. Out of eight S.aureus isolates, one has tst and VISA from vagina and the other one has tst, MRSA and VRSA from blood. Random Amplified Polymorphic DNA (RAPD) was chosen to represent S.aureus to be examined by Multilocus Sequence Typing (MLST)in which partial sequences for seven housekeeping genes (arcC, aroE, glpF, gmk, pta, tpi and yqiL) were provide a definitive Sequence Type (ST) for each strain. The comparison of NJ trees for each allele, has indicated the emergence of three new allele sequences (New Record of 3 Allele Sequences). Unrooted NJ tree showed four clades of high phylogenetic distances. Thus, there are either several different ancestors for these virulent clones or there are common mutants responsible for the phylogenetic variations among these strains.