The study was launched to estimate the genetic diversity and association mapping amongst Brassica juncea genotypes through agro-morphological traits. To estimate the genetic diversity data was recorded on 15 qualitative and 17 quantitative traits of 331 genotypes for two successive years. The recorded data was analysed through cluster and PCA. Valuable genetic variability was found for no. of days to physiological maturity, days to flowering and plant height. Pod shattering percentage have medium level of variation. Among the studied traits, highest and significant correlation (.97**) was recorded for days. to. flowering. initiation. and 50% days to flowering, flower initiation days and flowering completion days and days to half flowering and flowering completion days followed by correlation (0.89**) between flower initiation days and no. of days to physiological maturity. The genotypes studied were divided into 4 main groups based on cluster analysis. It was found that 6 out of 17 principal components with an eigenvalue of ≥ 1 accounted for 68.58% difference of the overall diversity found among the studied genotypes. The contribution of first 3 PCs in overall diversity was 30.63%, 10.30%, 8.92% respectively. For getting promising results, the elite genotypes could be recommended for future breeding programme. The association study exhibits identification of markers associated with economically important traits. A total of 131 B. juncea L. genotypes were used in the GWAS. Illumina® 90K Brassica Infinium Assay (~90,000 SNPs) were run on selected genotypes. Multiple SNPs distributed on most of the chromosomes were identified. A total of 366 significant loci (-log10 P-value ≤0.001)were identified for 17 economically important traits of Brassica juncea L. genotypes including, days to half flowering(DF50%),flowering completion days(DFC),no. of days to physiological maturity (DM), Pod shattering percentage (PS), Leaf length (LL), Leaf width (LW), Plant height (PH), No. of primary branches per plant (PB/P), Length of main raceme(MRL), Pods on main raceme(P/MR), Stem thickness (ST), Pod length (PL), Pod width (PW),no. of grains per pod (G/P),grain yield( GY/P), thousand seed weight ( TGW) and Blackleg in total of 77,969 SNPs with minor allele frequency (MAF) ≥ 0.05. 6, 6, 4, 8, 9, 8, 1, 1, 4, 6, 4, 4, 1, 10, 6 and 3 SNPs were identified on multiple chromosome locations for DF50, DFC, DM, LL, LW, PH, PB/B, PL, PW, Pod Shattering, ST, P/MR, S/P,GY/P,TGW and Blackleg, respectively. The discovered major SNPs could help breeders to select high performing Brassica juncea L. genotypes through marker assisted selection (MAS) as well as to develop elite lines for future breeding program.