The narrow genetic base of lentil (Lens culinaris) has challenged the efforts of breeders to increase its productivity under changing environmental conditions. Inclusion of wild species and diverse cultivated genotypes offers an opportunity to generate new variation through wide hybridisation to broaden the genetic base of cultivated lentil. We evaluated 96 elite, interspecific (L. culinaris × L. orientalis) and intraspecific advanced lentil genotypes along with four checks to determine the extent of genetic variation, resistance to lentil rust (Uromyces viciae-fabae), and the nature and magnitude of their genetic divergence. Sufficient genetic variability was revealed for all of the traits. High heritability and genetic advance were recorded for number of seeds per pod, number of pods per plant, seed yield per plant and biomass per plant. A positive correlation was recorded between grain yield and ten important plant traits. Statistical (D²) and molecular analyses grouped all genotypes into two main clusters and revealed sufficient genetic diversity among advanced lines. Our study showed promising results for creating new variation through wide hybridisation and identified lines L-354 and L-437-1 (rust-resistant) and HPLL-32 (moderately rust-resistant) superior for seed yield and related traits.