Information on the genetic structure of economically important fish species is essential for fisheries management and fish farming. DNA markers used in this study was successful in estimating genetic variation and species differentiation in four species of Egyptian tilapia and are of potential use in tilapia breeding programs. DNA profiles generated in each species of tilapia were unique. Genetic improvement of animals is limited by the fact that most traits of economically importance are polygenic in nature and are influenced by a variety of environmental and genetic factors. These markers can be used in monitoring QTL loci during selection programs. Markers linked to simple commercially important genetic traits such as disease resistance genes can also be identified from natural resources and introgressed into domestic strains. This study can be used as a baseline study for researcher and fish breeders who are interested in evaluating tilapia genetic resources and its potential use in developing selective breeding programs.