The experiment was carried out with a view to study the morphological and molecular characterizations under control and terminal drought conditions with 49 terminal drought tolerant groundnut genotypes. The experiment was carried out during kharif, 2016 in a simple lattice design at MARS, UAS Raichur. Data were recorded for different quantitative, physiological and quality traits. Analysis of variance revealed significant differences among the genotypes for all the traits studied. The dry pod yield, haulm yield, root volume, root dry weight, specific leaf area, SPAD chlorophyll meter reading, harvest index, root length, root diameter and root volume showed high PCV, GCV, heritability and high GAM under both conditions. The Mahalanobis’s D2 analysis revealed that 49 genotypes were distributed into seven clusters based on morphological data and cluster I contained maximum number of genotypes (23). The haulm yield and primary branches per plant contributed the maximum towards the divergence. The 27 groundnut specific SSR primers pairs were used for molecular characterization only seven primer pairs showed polymorphism between the test genotypes (25.92%). Six major clusters were formed at 0.82 coefficients of similarity and cluster III consists of maximum number of genotypes (18). The highly significant positive association recorded for kernel yield, haulm yield, root diameter and root dry weight with pod yield per plant at both phenotypic and genotypic levels under both conditions. The path analysis study indicated that high positive direct effect by kernel yield per plant on pod yield. The result of the aflatoxin quantification shows that aflatoxin content was more in terminal drought compare to control condition. Based on all the traits and drought tolerant indices for dry pod yield genotypes TAG-24, ICGV-07120, ICGV-13241 and ICGV-95440 considered as terminal drought tolerant genotypes. The above genotypes can be used as parental lines for the improvement of groundnut breeding programme.