Blackleg, caused by Leptosphaeria maculans is one of the most devastating diseases of canola (Brassica napus) in North Dakota. A study was conducted to characterize prevalence of pathogenicity groups (PG), identify population structure of L. maculans and identify sources of resistance among B. juncea accessions. Approximately 56% of the isolates belonged to PG-4, 13% to PG-3, 11% to PG-T, 5% to PG-1, and 2% to PG2. The remaining 13% of isolates could not be identified. The 605 single-spore cultures used to study the population genetics of L. maculans in ND were grouped according to their county of origin in five regions (NE, NC, NW, WC, and C) and each region was considered a population. These populations were tested for genetic variation at 7 microsatellite, 4 minisatellite, and for mating type loci. High levels of genetic diversity (H = 0.63 to 0.70) and significant gametic disequilibrium (P < 0.001) was observed in all populations. The ratio of mating type idiomorphs deviated significantly (P < 0.05) from 1:1 ratio for four populations. Highly significant (P < 0.001) G''ST between pairs of populations indicated a strong population differentiation. STRUCTURE analysis identified three distinct genetic populations in which the majority of the isolates from WC and nearly half of the isolates from NC were assigned to subpopulation one. The remaining half of NC isolates were assigned to subpopulation two and rest were assigned to subpopulation three. To identify sources of resistance against PG-2, PG-3, PG-T, and PG-4, a set of 298 B. juncea accessions were screened in greenhouse trials. Six accessions were resistant to PG-2 and PG-3, nine accessions were resistant to PG-T and PG-4, and two accessions were resistant to PG-2 and PG-4. DNA extracted from these accessions was screened using 766 DArT markers to identify QTL associated with resistance. Thirteen DArT markers were significantly (P<0.05) associated with resistance to PG-2 with variability ranging from 0.9% to 6.4%. Of these, three were also found significantly (P<0.05) associated with resistance to PG-3 with variability of 4.4%. No markers were found to be significantly associated with resistance to PG-T or PG-4 at (P<0.05).