Bignoniaceae is an important component of neotropical forests and a model for evolutionary and biogeographical studies. A previous combination of molecular markers and morphological traits improved the phylogeny of the group. Here we demonstrate the value of next‐generation sequencing (NGS) to assemble the chloroplast genome of eight Anemopaegma species and solve taxonomic problems. Three NGS platforms were used to sequence total DNA of Anemopaegma species. After genome assembly and annotation, we compared chloroplast genomes within Anemopaegma, with other Lamiales species, and the evolutionary rates of protein‐coding genes using Tanaecium tetragonolobum as the outgroup. Phylogenetic analyses of Anemopaegma with different data sets were performed. Chloroplast genomes of Anemopaegma species ranged from 167,413 bp in A. foetidum to 168,987 bp in A. acutifolium (“typical” form). They exhibited a characteristic quadripartite structure with a large single‐copy region (75,070−75,761 bp), a small single‐copy region (12,766−12,817 bp) and a pair of inverted repeat regions (IRs) (39,480−40,481) encoding an identical set of 112 genes. An inversion of a fragment with ca. 8 kb, located in the IRs and containing the genes trnI‐AAU, ycf2, and trnL‐CAA, was observed in these chloroplast genomes when compared with those of other Lamiales. Anemopaegma species have the largest genomes within the Lamiales possibly due to the large amount of repetitive sequences and IR expansion. Variation was higher in coding regions than in noncoding regions, and some genes were identified as markers for differentiation between species. The use of the entire chloroplast genome gave better phylogenetic resolution of the taxonomic groups. We found that two forms of A. acutifolium result from different maternal lineages. Ver menos