The maize race Tuxpeño is well known by breeders as tropical late white dent with cylindrical productive ear shape.  It has produced useful varieties, lines, and hybrids in many parts of the world. We have developed a Tuxpeño core (321 out of 1350 Tuxpeño accessions) based on phenotypic diversity among the Tuxpeño collection preserved at CIMMYT.  In order to exploit Tuxpeño core collection in making targeted breeding crosses and line development work, molecular characterization was done for 660 plants of the Tuxpeño core, 4 U.S. and Chinese temperate lines, 54 U.S. Germplasm Enhancement of Maize lines (GEM), and 94 CIMMYT maize lines (CML). Two plants of each Tuxpeño accession were genotyped using 1433 Single Nucleotide Polymorphism (SNP) markers. First, a minicore subset (20%) of Tuxpeño Core with the size of 64 was developed to represent its diversity based on both phenotypic (44 traits) and genotypic data (SNP data).  Second, using 1041 out of 1433 SNPs, the modified Rogers distances (MRD) and allele frequency differences among Tuxpeño core, heterotic groups of CML-A (dent), CML-B (flint), GEM-SS (stiff stalk), and GEM-NSS (non stiff stalk) were assessed. Tuxpeño core had no absent alleles but CML and GEM did. GEM-SS had clearer separation from GEM-NSS. Tuxpeño core had much less MRD from CML-A, CML-B and GEM-NSS as compared to the distance between it and GEM-SS. Allied breeding cross combinations between GEM-SS and CML-A (or Tuxpeño minicore), and between GEM-NSS and CML-B (or Tuxpeño minicore) can be made to exploit untapped genetic diversity present in Tuxpeño core. In the same way, Tuxpeño minicore can be used for enhancing preferably CML-A and CML A/B. Selection for adaptation and increasing genetic divergence among heterotic groups are of primary importance in the proper breeding procedures for development of superior lines and hybrids.