Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into an existing breeding pool, several generations of selection against poor performance must follow crosses between exotic germplasm and elite breeding material. Selection may result in a substantial loss of exotic alleles, either because of their contribution to poor agronomic performance and adaptation or linkage to such alleles. The objective of this study was to estimate the percentage of alleles derived from exotic germplasm within S₂-lines developed from breeding crosses among Caribbean and Mexican landraces and late yellow CIMMYT maize lines (CMLs). Six S₂-lines, their CML parents four bulks of the breeding pools the CMLs were drawn from (Pools 25 and 26, 15 individuals per bulk), and four bulks of each landrace parent were characterized using 27 SSRs. The six S₂-lines were equal or superior to hybrid checks for agronomic performance and disease resistance in CIMMYT topcross evaluation trials in 2001. The percentage of detectable exotic alleles in the S₂-lines ranged from 5 to 23%, with a mean of 17%. These are lower bound proportion estimates as on average 73% of the alleles were shared among CMLs and landraces. In a cluster analyses based on modified Roger's distance each landrace formed a distinct cluster. S₂-lines clustered together with the CMLs but separately from both pools 25 and 26. These results indicate that maize landraces harbor alleles that improve productivity of elite materials and may be tapped via backcrossing. S₂-line development from breeding crosses represents a good method to incorporate this new diversity into available breeding pools.