The exploration of genetically variable accessions is the key source of germplasm conservation and potential breeding material for the future. The more diverse group of cultivars can provide an ample opportunity to breeders for releasing new and superior varieties, considering their quality traits for direct commercial utilization. In advanced research studies the polymerase chain reaction (PCR) based molecular markers have a great contribution in genome analysis and marker-assisted selection. In this study, the genetic diversity of Cicer arietinum L. twenty four indigenous and forty six exotic accessions were assessed, obtained from plant genetic resource institute (PGRI), national agriculture research centre, Islamabad, Pakistan. These accessions were planted under field conditions at research area of University of Malakand, Chakdara, Khyber Pakhtunkhwa. The genetic diversity among seventy chickpea indigenous and exotic accessions was estimated using morphological, biochemical; sodium dodecyle sulphate polyachryl amide gel elecctrophoresis (SDS-PAGE) and molecular markers; random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. Based on qualitative and quantitative morphological traits, the average coefficient of variation (%) was calculated 44.8% and 56.8% respectively with significant correlation among yield traits. The analysis revealed that the accessions 1898, 2819, 3022, 3037, 3040, 3043, 3054, 3059 and 3063 were best in performance with a total of 12% environmental error. The statistical analysis showed that 100 seeds weight was significantly correlated with seed size quantitatively. The majority of accessions of USA origin were observed with maximum100 seed weight (30-57gm) and medium to large (7.2- 9.9mm) size seeds including one of the Pakistani accession 2562 also with large size seeds. The wilt incidence (%) was observed to be comparatively higher (30 - 42.85% ) at both growth stages in field screening of the germplasm than that of greenhouse conditions; reduced up to 8.57% at seedling stage and 24.28% at reproductive stage. The t-test however, indicated that chickpea both from indigenous and exotic origin showed a significant variation at alpha ≤ 0.050 at seedling and reproductive stage. The cluster analysis based on protein data indicated 50% genetic diversity among the accessions. The clustering pattern did not reveal any grouping that could be attributed to either the geographic distribution or the field performance. For molecular characterization of xiv germplasm twenty random amplified polymorphic DNA (RAPD) and twenty simple sequence repeat (SSR) polymerase chain reaction (PCR) based markers were screened for estimation of genetic variability. In the markers, five random amplified polymorphic DNA (RAPD) and fifteen simple sequence repeat (SSR) were polymorphic and showed significant level of coefficient of variation. The data of molecular markers were scored by the presence (1) and absence (0) of allele and subjected to statistical analysis. The analysis was based on coefficient of molecular similarity using un-weighted pairs group mean average (UPGMA) resulted in 37% and 55% genetic diversity among the total germplasm using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers respectively. For marker trait association analysis, twenty random amplified polymorphic DNA (RAPD) and twenty simple sequence repeat (SSR) makers were utilized to find correlation of markers with yield contributing components and chickpea Fusarium wilt resistant genes. None of the random amplified polymorphic DNA (RAPD) primers were linked to seed size and seed weight while, simple sequence repeat (SSR) markers TA72 and TA130 showed association at linkage distance 0.4 with seed weight and seed size. Based on which the high yielding accessions among chickpea germplasm were identified. Hence, the association of these makers is helpful for the plant breeders to select lines on the basis of yield contributing traits. Among the total used random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) primers, TA194 (SSR marker) was linked to the disease response with 85% probability level. This association or correlation of the marker was reconfirmed by receiver operating characteristic curve (ROC). Hence, the use of the sorted wilt resistant genotypes through simple sequence repeat (SSR) marker TA194 can make available ample prospect in marker assisted breeding for yield improvement of chickpea in Pakistan.