Sugarcane is one of the most genetically complex species. It is both aneuploid and polyploid with a large number of chromosomes. Consequently, simply inherited traits are rare; only five have been identified to date of which four are disease-related (including rust resistance) and one is a morphological trait. The genetic complexity and large genome size of sugarcane, together with the Jack of a close diploid relative, make map-based gene cloning in sugarcane a challenge. This chapter outlines the strategies developed to overcome these difficulties and describes progress towards the cloning of a durable rust resistance gene. Using syntenic relationships with model crops (sorghum and rice), enriched BAC libraries and haplotypespecific chromosome walking, a high-density genetic map and a partial physical map of the region surrounding the rust resistance gene has been developed. A comparison with other homo(eo)logous chromosomes at this region reveals the presence of a large insertioncurrent efforts are focusd on characterizing and walking through the insertion.