The present investigation was carried out to detect the variation in the morphometric characters and also by the biochemical methods (protein and enzyme profile) of Penaeus semisulcatus. A set of four morphometric variables, the depth of the abdomen (SSD) at the mid-point of the sixth segment; depth of the abdomen (SAD) at the intersection of the second and third segments, partial carapace length (PCL) from the posterior margin of the orbit to the posterior edge of the carapace; width of the carapace (CW) at the point of the last dorsal rostral tooth were measured. Among the four variables measured sixth segment depth (SSD) showed the highest correlation with the tail weight (TLW). Considerable differences are not seen, indicating the samples collected from Kochi and Calicut belongs to a single morphological stock .Biochemical analysis of protein and enzymes - Aldehyde oxidase (AO), Aldolase (FBALD), Octanol dehydrogenase (ODH), and Esterase (EST) by Polyacrylamide Gel Electrophoresis (PAGE) was conducted on P. semisulcatus collected from selected landing centres such as Kochi and Calicut of west coast of Kerala. Considerable differences in banding patterns were not found in the stocks obtained from Calicut and Kochi and can be related to the fact that the genetic makeup is similar (Homozygous).