Many germplasm of Pisum sativum have been screen for estimation of genetic diversity, cluster plating and gene linkages. Little attention has been given to the development of homozygous lines from single seed descent method in pea. In the present study 24 pea lines were evaluated, out of 24 lines, 20 pre-developed novel lines of Pisum sativum were achieved through single seed descent method from the cross of Falloner and 11760-3ER. In parental combination, Falloner (female) was dwarf, bushy tendrils, leafless, no anthocyanin pigmentation, creamy flower, green pod, creamy seed color, smooth seed shape, disease resistant and low yielding. Whereas, 11760- 3ER (male) was tall, normal tendrils, leaflet present, anthocyanin pigmentation present, purple flower, purple pod, brown seed color, rough seed shape, disease susceptible and high yielding. The control lines for comparative performance was Climex (PL-22) and local cultivar (PL-21). All the selected pea lines were evaluated through morphological and molecular markers in order to select high yielding and powdery mildew resistant novel lines. These lines were further screened for estimation of genetic diversity and genetic linkages. In morphological traits analysis 9 qualitative and 22 quantitative traits were studied. Based on quantitative traits analysis, two novel high yielding and disease resistant pea lines (PL-4 and PL-5) were selected for seed certification. The grain yield of PL-4 and PL-5 is significantly (p< 0.05) high as compared to PL- 21 and PL-22. Regarding traits association, "seed coat with anthocyanin pigmentation" showed genetic linkage with "pigmentation on flower and leaf axil" and vice versa. Interestingly, the cluster analysis grouped "tall/low yielding", "dwarf/low yielding", "tall/high yielding", "dwarf/high yielding" pea lines independently. For molecular characterization, 20 RAPD and 85 SSR markers were screened to estimate genetic diversity and genetic linkage. The RAPD markers amplified 69 bands out of which 95.6% bands were polymorphic. The similarity indexes were ranging from 0.43 to 0.88%. Furthermore, out of 85 SSR markers, 12 showed genetic polymorphism and produced an average of 2 alleles per SSR locus. The polymorphism information content (PIC) values of SSR markers ranged from 0.08 to 0.47, with an average of 0.33. Nei’s genetic distance (GD) between accessions ranged from 0.10 to 0.92. Among the total used SSR primers, only P628 SSR marker showed significant linkage with grain yield traits at 90.91% probability. The linkage of the marker was reconfirmed through Chi-square test and showed r = 0.918 (P ≤0.00) genetic linkage. This markers can be directly utilized in MAS breeding for the selection of high yielding edible pea lines.