Previous work revealed that the simple sequence repeat (SSR) markers SSRY 28 and NS158 are the closest markers to the gene CMD2, which confers a high level of resistance to cassava mosaic disease (CMD); they are located at distances of 9 and 7 cM, respectively. High resolution of the CMD2 region of the genome was initiated in this region to identify markers more closely linked to CMD2. The fine-mapping population was 1690 individuals from a cross between TME3, the source of CMD2, and improved variety TMS30572. The cross was evaluated in the 2002 growing season for CMD resistance in the field at the International Institute for Tropical Agriculture (IITA) Ibadan, under heavy natural pressure of the disease. The population was evaluated with two simple sequence repeat (SSR) markers, and a total of 112 recombinants between the markers and CMD2 were identified. DNA from 10 resistant recombinants and 10 susceptible recombinants were combined to form two bulks, which were then evaluated with several marker systems including amplified fragment length polymorphism (AFLP), ISTRs, random amplified polymorphic DNAs (RAPDs) and SSRs in a modified bulk segregant analysis (BSA). Markers that were polymorphic in the recombinant bulks were then analysed in individuals of the bulks. Two polymorphic RAPD markers were identified. One, RME-1, is 4cM from the gene; it was cloned and converted into a sequence-characterized amplified region (SCAR) marker. A bacterial artificial chromosome (BAC) library with more than 10x coverage for the cassava genome was constructed from the cassava variety TME3, donor parent of CMD2. The TME3 BAC library is made up of 73,728 clones in 192,384 well plates. The insert size ranged from 20 kb to 130 kb with an average insert size of 100 kb. The BAC library was screened with polymerase chain reaction (PCR) amplification of BAC pools using SCAR marker RME-1 yielding 34 positive clones and SSR marker NS158 yielding 2. NS158 is a single-copy SSR marker while RME1 was developed from a multiple-copy RAPD marker. The clones were digested with 20U of HindIII overnight and run for 24 hours on 1.2% agarose gel to obtain a BAC clone. Contig construction was by the FPC program. Primers will be designed from the end of the BAC clones that make up the extreme of the contigs and mapped in a set of recombinants from the fine-mapping population. The new markers will be used in another round of screening of the BAC library and a ‘walk’ to the CMD2 initiated. Successive hybridizations of the BAC end markers to the BAC library will be carried out until markers that flank the gene on both sides are identified.