The environmental heterogeneity may reflect the different morphological and phenotypic traits of individuals belonging to a single species. We used 14 morphological traits of Mauritia flexuosa L.f. to understanding the relation between environment and phenotypic traits. Twenty-five fruits were collected from each of the 10 individuals sampled in each study site: Chapada dos Guimarães (CG), Vila Bela da Santíssima Trindade (VB), and Alta Floresta (AF). We analyzed the genetic divergence, using the standardized Euclidean distance, the sequential method of Tocher, unweighted pair group method with arithmetic mean (UPGMA), and the projection of the distances onto 2D plane, and calculated the relative importance of the traits evaluated. The analysis showed the partition of individuals into three main groups: Two groups comprising the majority of individuals. Fresh fruit weight, pulp rate, fresh pulp weight, and moisture rate were the traits that most helped explaining the difference between materials. The results shown in the current study evidenced the influence of these three different environments on the biometric traits of M. flexuosa. Such influence has led to the formation of Alta Floresta and Vila Bela da Santíssima Trindade individuals in different groups, whereas the Chapada dos Guimarães individuals were able to permeate the two other groups, although they showed stronger tendency to group with individuals from Vila Bela da Santíssima Trindade.