We compared the diversity and species composition and the structure of the vegetation of three distinct Cerrado phytophysiognomies (Cerradão, Dense Cerrado, and Typical Cerrado) in the Cerrado–Amazon transition, Mato Grosso (Brazil). Species richness (observed and estimated) in the Cerradão and Dense Cerrado was higher than that recorded in the Typical Cerrado. Species diversity, based on a Rényi profile, was highest in the Dense Cerrado, in comparison with the other phytophysiognomies. We recorded a higher number of exclusive species in the Cerradão and a greater similarity (Morisita and Sørensen indices) between this vegetation type and the Dense Cerrado. While individuals were tallest in the Cerradão and Dense Cerrado and lowest in the Typical Cerrado, there was no difference among phytophysiognomies in mean diameter. A gradient in decreasing species richness and diversity (hypothesis 1) and vegetation vertical structure (hypothesis 3) was expected for the Cerradão–Dense Cerrado–Typical Cerrado; however, neither hypothesis was supported by the results. The Cerradão and Dense Cerrado were most similar in species composition not confirming hypothesis 2, which predicted that the two savanna vegetation types (Dense Cerrado and Typical Cerrado) were more similar to one another than either is to the woodland (Cerradão). Overall, the similarities among the three study communities depended on the type of parameter analyzed. While the species richness and the vertical and structure of the vegetation of the Cerradão and Dense Cerrado are closely similar, the Cerradão and Typical Cerrado are more similar in their species diversity. With regard to the floristic composition, Dense Cerrado occupies an intermediate position between Cerradão and Typical Cerrado.