Genetic gains being achieved in the Canal Point sugarcane (Saccharum spp.) breeding program implies that the relevant genomic regions are being effectively targeted. This study evaluated the role of breeding in shaping the patterns of genetic diversity and structure in this program and consequently identified loci putatively under selection. Using a dominant marker system (Target Region Amplified Polymorphism/TRAP), 61 genotypes (six wild progenitors, eight hybrid founders, and a mix of 47 cultivars-breeding lines going from 1955 to 2000) were divided into seven populations/decades and scored with 24 primers. Mean genetic diversity (HE) was around 0.23 across decades. With allele frequencies calculated by the square root method, there were reductions in HE (0.02 decade-1), in number of alleles (21 decade-1), in percent polymorphism (6%), indicating that plant breeding has reduced the levels of genetic diversity in sugarcane. Most (96%) of the genetic variance was among individuals and little (4%) differentiation among decades, an evidence of homogenization by constant gene flow. Bayesian analyses gave also evidence of differentiation among decades, but of a milder reduction in HE (0.003 decade-1), suggestive of a population bottleneck. Highly significant (P<0.001) linkage disequilibrium (IAS) between loci was detected within each decade and at the population level. IAS fluctuated over the course of the breeding generations, with a large drop (from 0.0121 to 0.0026) from the progenitor to the founder population, a sharp increase thereafter up to 0.0139 in the 4th decade, and another drop to 0.0009 or to 0.004 in the 6th or 7th decade, respectively. Coalescent simulations yielded 15 loci as putatively influenced by selection, by falling below the lower limit of the 95% quantile, i.e. outside the expected distribution region of neutral loci. Stabilizing selection and drift were the primary causes of maintaining polymorphisms in this breeding program.