Cassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary source of food and income. However, cassava production is threatened by several viral diseases, including cassava brown streak disease (CBSD), which causes severe damage to the edible storage roots. Current cassava varieties in Africa lack effective resistance to this disease, leading to significant crop losses. We investigated the genetic diversity of cassava and identified new sources of resistance to the viruses causing CBSD. The cassava line, COL40, from a South American germplasm collection showed broad-spectrum resistance against all known strains of the viruses that cause this disease. To further understand the genetic basis of this resistance, we sequenced the genome of COL40 and produced a high-quality, haplotype-resolved genome assembly. This genomic resource provides new insights into cassava's genetic architecture, particularly in regions associated with disease resistance. The sequence reveals significant structural variation, including transposable elements, inversions, and deletions, which may contribute to the resistance phenotype. The reference genome assembly presented here will provide a valuable genomic resource for studying the cassava brown streak resistance and will help in accelerating breeding efforts to introduce virus resistance into African cassava varieties. By identifying genetic variants linked to resistance, future breeding programs can develop cassava cultivars that are more resilient to viral threats, enhancing food security and livelihoods for smallholder farmers across regions affected by the disease.