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Background: Maize (Zea mays L.) is the main sustenance in the daily diet of Mexican families. As a crop, it is one of the most important in the country of Mexico, and in Yucatan state, it is grown under rainfed conditions in milpas with no mechanizable lands. In this study, an analysis of the phenotypic variability from cob collects of native maize from Yucatan state was carried out, with ethnobotanical information collected within passport data. Objectives: To introduce the genetic diversity of maize into a germplasm bank, to know the genetic diversity of native populations based on the characteristics of cob, to know its distribution, to find the potential populations in each collection area for its use in genetic improvement programs. Methodology: 66 Tuxpeños, 13 Dzit bacal, 6 Nal tel, 13 Xmejen nal, and 2 Nal xoy were collected in the southern, central, and eastern regions of the state, from January to March 2020, by sampling the four cardinal points in each community visited. A vector map of collections in Yucatan was developed and quantitative data of 13 biometric cob variables were recorded in 100 populations (crop cycles: late n=68; intermediate n=26; early n=6), a general data analysis of variance (ANOVA) and by crop cycles were made, principal component analysis (PCA), hierarchically clustered with the average linkage method and discriminant analysis were made. Qualitative data from ethnobotanical surveys with mixed questions applied to milperos at the time of collection are presented. Results: The diversity of native maize in Yucatan is made up of three main groups based on the crop cycle: late, intermediate, and early. The southern and eastern regions of Yucatan preserve greater diversity, representing 44 and 40% of the total collections, respectively. There were significant differences in all ear variables; in a late growth cycle, only the grain thickness did not show differences between populations, and in the early growth cycle the grain thickness, width, and length variables were not significant. The PCA explained 80% of the total variation, seven different groups were formed, with greater differentiation in early maize Nal tel, intermediate Xmejen nal and Dzit bacal, contrary to the Tuxpeños late maize. Ten promising populations were identified for selection in each geomorphological region: eight correspond to the southern, two to the eastern, and one to the center of Yucatan state. The main factors to select for sowing corn in the region are: white and yellow maize for yield, the resistance to weevil attack for red maize, and the perception of color and palatability in purple maize. Implications: A complete phenotypic characterization in the field is required with a special interest in red-pigmented maize. Conclusions: The interest of the milperos in conserving and sowing the different native maize are based on the color of the grain, the benefits and uses that they can obtain from them, which determine the planting area in the milpas of the different races/varieties of maize. Red grain maize is being planted in a lower area in relation to other colors. The southern and eastern geomorphological regions showed a genetic flow between them.