The wild species of the genus Zea comprise nine different taxa, including annual and perennial, diploid and tetraploid species, distributed from northern Mexico to Costa Rica. Due to the great variability existing among species, the aim of this work was to evaluate the morphological and climatic variability patterns and phylogenetic relationships among species, based on morphological characters. Two hundred and seventy-six populations of known species and races were included; 15 individuals per population were planted. From each individual, 19 morphological and physiological traits were measured, and at each collection site 23 climatic descriptors were obtained. Both data sets were analyzed with multivariate analysis. For the phylogenetic analysis 17 morphological variables were transformed to character states using GAP-WEIGHTING. With multivariate analyses, it was possible to determine the existence of well-defined groups. Species, and races of different subspecies, were found to be clearly delimited by geographic regions, climatic characteristics, altitudes, and distinct morphological features. The phylogenetic relationships found are congruent with those identified in similar studies based on molecular data. Morphological data on their own cannot give enough information to infer divergence times. In this context, multivariate and phylogenetic analyses with morphological data are taxonomically of great importance for identifying species and subspecies of genus Zea. At species level, the study has added elements to distinguish between Zea diploperennis from the states of Nayarit and Jalisco, between Zea perennis from Michoacán and Jalisco, and between Zea luxurians from Oaxaca and Guatemala.