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Characterizing the genetic diversity of maize (Zea mays L.) populations by their morphological and molecular attributes makes it possible to place populations into specific groups, thus, facilitating the design of procedures for their optimum and sustainable use. In this study, data from two lines of evidence were analyzed simultaneously to robustly classify maize populations and to determine their genetic relationships. Seven maize races of the central high plateau of Mexico were characterized using a combined analysis of 13 morphological traits and 31 microsatellite loci. The germplasm assessed included samples of 119 accessions held at Mexican germplasm banks. Cluster and principal component analyses were performed. Also, genetic and geographic relationships among the accessions were determined. Principal component analysis separated the different accessions into well-defined groups using first three principal components. The accessions of Arrocillo Amarillo and Elotes C&oacute, nicos races did not exhibit a grouping pattern, indicating greater genetic complexity. Better grounded grouping and phylogenetic relationships were obtained when traits of both lines of evidence were used simultaneously.