Abstract: Melia dubia is a large perennial deciduous tree with medicinal and economic importance. The present study aimed to evaluate physical and biochemical variability of Melia dubia collected from three different states viz., Karnataka, Kerala and Tamil Nadu in India. One hundred seeds of Melia dubia were randomly collected from Chamraj nagar, Chikkahole, Pannampalli, Thalamalai and Theni region of three states. The variability of physical parameters was analyzed by Lecia QWin image analyzer and also determined biochemical parameters. The results revealed that Melia dubia from Chickkahole region showed maximum amount of area, length, perimeter, equivalent diameter, curve width and convex area was compared to other sampling areas. According to the biochemical proximity studies, Chamraj nagar and Theni showed the highest level of amino acids and protein content. This study concluded that physical and biochemical character plays a part in the selection and migration of seeds for improved germination and afforestation.