Native polyacrylamide gel electrophoresis was used in the current study to identify polymorphism in α- and β-esterase loci in leaf tissues of wild poinsettia plants for the analysis of genetic diversity and structure of populations. Seeds were collected from different plants in 12 different populations. Two to three allelic variants were at Est-1, Est-2, Est-3, Est-4, Est-5, Est-6, and Est-7 loci. The estimated proportion of polymorphic loci in populations is 87.5%. High and low values of observed and expected proportion of heterozygous loci in 12 populations confirm our suspicion that the populations are genetically structured (FST = 0.1663). The heterozygous deficiencies are evidenced by the positive value of FIS (0.1248). The positive FIS value indicates a deficit of heterozygous (12.48%) or an excess of homozygous plants, which could be the result of frequent herbicide application in areas where seeds were collected and/or the result of self-pollination. Overall inbreeding or nonrandom breeding, according to the significant FIT value (0.2703), did play a major role in shaping the genetic structure of these populations. Identity values represented in the dendrogram should play a more central role in developing policies to manage and control this species.