Naphthoquinones isolated from the wood of trees of the families Bignoniaceae and Verbenaceae have been subjected to an interdisciplinary study since the seventies, when Dr. Benjamin Gilbert, at the Federal University of Rio de Janeiro, launched a program on the chemistry of natural products active against endemic diseases. In this paper we describe the synthesis of five naphthoimidazoles, derived from this program and their activity towards T. cruzi, the etiologic agent of Chagas disease. We also review the influence of chemical structure on trypanocidal action of naphthoquinones and of derived heterocycles with imidazole, oxazole, phenoxazine, indole, dipyrane and cyclopentene rings. The overall analysis corroborates the tendency of trypanocidal activity in compounds with an imidazole or oxazole ring linked to a naphthopyrane structure. Two naphthoimidazoles presented higher activities (14.5x and 34.8x) than the standard crystal violet. Emphasis is given to the biodiversity of the Brazilian flora as a starting point for the development of an autonomous and creative medicinal chemistry.