The seed storage free amino acids of 4 taxa of Blyxa were analyzed from the fully aquatic family Hydrocharitaceae by Thin Layer Chromatography. Total 22 amino acids were found, among these 3 were not identified. Considerable amount of homology were observed in between Blyxa aubertii var. aubertii and B. aubertii var. echinosperma (60%). Also another homology observed in between B. octandra and B. quandricostata (41.17%), but B. japonica was far differ from others analyzed taxa. The major amino acids were Amino-n-butyric acid, Glutamic acid, Phenylalanine, Glycine, Tryptophan, Methionine, Isoleucine and Serine. The present observation reveals that there was a correlation in between morphology and free amino acids composition of Blyxa analyzed taxa. Free amino acids can use as a taxonomic markers to draw the similarity among the plant taxa.