The present study entitled as “Diversity in Lentil (Lens culinaris M.) based over Morphological and Molecular Markers” was carried out using 30 diverse varieties/strains for seed yield and its components. The material was planted during rabi, 2013-14, at Rajasthan College of Agriculture, Udaipur and Agriculture Research Station, Kota. Observations were recorded for 10 yield contributing characters and seed protein content. Genetic divergence [15] was computed for each location separately and over pooled basis. DNA was isolated with CTAB extraction buffer method. DNA concentration and purity was checked by spectrophotometer and agarose gel electrophoresis. Isolated DNA was used as template for amplification of DNA using 20 randomly selected decamer primers. To conclude, characters 100-seed weight followed by pods/plant and biological yield/plant contributed maximum towards divergence at both locations and over pooled analysis. Based over field studies conducted over 2 locations, divergent and high yielding genotypes in clusters VI/VII/I (RKL 603-1, IPL406, RKL 606-09, DPL-62, RKL1003-59F, RKL1017, RKL1003-53E, RKL1003-44E and RKL1003-46E) were identified. It is interesting to record that using RAPD analysis, above genotypes were also classified as most divergent belonging to different clusters.