MultiLocus Sequence Analysis(MLSA)is a current and meanwhile largely used method in order to obtain a higher resolution of phylogenetic relationships of species within a genus or genera within a family,In MLSA studies,partial sequences of genes coding for proteins with conserved functions(housekeeping genes)are used to generate phylogenetic trees and subsequently deduce phylogenies.MLSA has been initially not only suggested as a phylogenetie tool to support and clarify the resolution of bacterial species with a higher resolution as 16S rRNA gene based studies,but was also discussed to replace DNA-DNA hybridization(DDH)for species delineation.But despite the fact,that MLSA became an accepted and widely used method in prokaryotic taxonomy,no common and generally accepted recommendations have been devised so far,neither for the whole area of microbial taxonomy,nor for taxa specific applications of individual MLSA schemes.The ways,MLSA are performed can strongly vary in the selection of genes,the number of selected genes and the mode of calculations when comparing the obtained sequences.In this lecture the current application of MLSA in prokaryotic taxonomy showing pro and cons,advantages and disadvantages of this method with its numerous variations will be reviewed with the aim to give a perspective for its future use in upcoming genome based genotypic taxonomic analyses.