Traditionally, the prediction of hybrid performance made on the basis of the morphological traits requires large number of crosses to be made, which have several associated problems. This is where molecular markers will be handy in determining genetic diversity and this will help in predicting hybrid performance. An essential assumption underlying the use of DNA markers for predicting hybrid performance is that a strong linear correlation exists between heterozygosity and heterosis (Singh et al., 2006). Hence, the investigation of correlation existed between "Molecular marker polymorphism and hybrid performance? was undertaken in terminal water stress condition in pearl millet for yield and drought resistance traits.We have tried to investigate the above assumption by using molecular markers (RAPD & SSR) diversion and morphological diversion (Mahalanobis's D2 clustering ) and its correlation with heterosis (MPH, BPH) in pearl millet. Detail results are presented and discussed here in this book, provides insight about the correlation existed between diversity and heterosis in pearl millet.