Forage and grain maize has been widely cultivated in central highland of Mexico; however little is known about the amount and distribution of genetic variation within and among adapted inbred populations. We evaluated 328 inbred lines (ILs), originally maintained from 27 singled crossed races representing the most prominent Mexican tropical, highland and temperate races. 49 SSR pair primers were used to determine the phylogenetic relationship among ILs by molecular data. In addition, we established the ILs in two locations in 2004 and estimated the genetic variance components, genetic correlations, narrow sense heritability and genetic diversity of 15 morphological traits. Genotypic effect were highly significant for all investigated morphological traits (P<0.001), and higher than genotype x environment effect interaction in all tropical ILs, but only higher in two of four highland ILs. Heritability ranged from 0.2 to 0.6. Mean genetic diversity (Jaccard coefficient) was 0.59 among ILs for the morphogical traits, clustered the ILs into 3 groups. The 49 SSR detected 156 alleles, with a range per locus from 2 to 7 (avg 3.19). The PIC values per locus ranged from 0.09 to 0.75 (avg 0.48). On the basis of the marker analysis the ILs were classified also into three distinct clusters, which represent tropical races, highland and temperate races and mixed ILs, respectively. Significant correlations was identified between genetic distance and tropical and temperate races for both morphological and molecular data. In addition, we chose 8 contrasting ILs by the genetic diversity of both morphological and molecular data, and they were crossed in a partial diallel design. Morphological data are presented on the heterosis basis and compared to the original selection by marker data. We concluded SSR markers and morphological data can be complemented to dissect genetic diversity and select heterotic groups.