Effect of EMS (ethyl methane sulphonate) on induced morphological mutants and chromosomal variation in cowpea was studied using five different doses of mutagen along with a control in randomized blocked design with three replications. The morphological mutants there are two types of viable and chlorophyll mutants. Viable mutant contains tall, dwarf, early maturity, late maturity, leaf mutants pod mutant and flower mutants. The frequency of chlorophyll mutant contains albino, xantha and viridis. This concentration can damage or modify important components of plant cells and have been reported to affect the morphology, anatomy, biochemistry and physiology of plants differentially depending on the concentration level. These effects include changes in the cellular structure and metabolism of the plants eg, dilation of thylakoid membranes, alteration in photosynthesis, modulation of the antioxidative system and accumulation of phenolic compounds. The morphological and chromosomal variation was found to be mutagen sensitive in somatic cells of cowpea. It was found to increase with increasing the concentration of EMS in Cowpea plants. The chemical mutagen like ethyl methane sulphonate induces high frequency of chromosomal changes like anaphasic bridge; anaphasic laggard, anaphasic bridge and clumbing of chromosome were including control plants also observed.