This book has been cataloged the different Artemia populations are confined to solar salt pans where present along the Southeast coast of India. The survey included Artemia populations from Kelambakkam, Tuticorin, Vedaranyam and Thamaraikulam in South India. The research also studied the morphometric characteristics of adult Artemia, furcal morphology,cyst biometry and architecture of cyst membrane. On scanning electron microscopic observation, the cysts of all populations showed almost similar surface topography. However, the furcal morphology clearly indicated subtle variation among the populations studied. Further, molecular genetic characterization of populations was done using RAPD finger printing technique. A novel 16S rRNA\tRNA-Val mitochondrial region was sequenced and subjected to restriction digestion analysis in order to elucidate the phylogenetic congruence of Artemia populations. The obtained with the following GeneBank accession numbers: KBM strain (HQ840435), VDM strain (HQ840436), TCN strain (HQ840437) and TKM strain (HQ840438) nucleotide sequences were compared with other sequences available at the GeneBank database.