The greatest challenge to the modern plant systematist is the interpretation of molecular phylogenies that do not correspond to previous classifications based on morphological data. Characters that on first appearance seem highly diagnostic are brought into focus by phylogeny and frequently shown to have evolved multiple times independently. Parallelism is usually neglected in such systematic studies and the homoplastic distribution of a character in a phylogeny is commonly accredited to convergent evolution. The impact of parallel evolution on angiosperm systematics is examined here using a taxonomically complex and species-rich group of tropical tree genera (Myrcia, Marlierea, Calyptranthes; Myrtaceae) as a case study. These groups are traditionally distinguished by flower characters and have been shown to be polyphyletic by molecular data. Floral ontogeny of distinct lineages is examined using SEM and plotted on a five gene phylogenetic hypothesis to estimate ancestral states and phylogenetic signal for developmental variation. Results show that floral characters responsible for taxonomic confusion are a result of both parallel evolution and convergence. This is contrasted with other diverse and taxonomically complex angiosperm groups and problematic taxonomy appears linked to recent diversification events where the same genetic basis remains latent, demonstrating parallelism to be an important factor in problematic taxonomies. In this study, variations in early stage floral development produce the most labile characters. This is discussed in light of ontogenetic patterns in angiosperms with focus on the evolutionary consequences of homoplastic variation during early vs late floral development. The prevalence of parallelism must be appreciated by taxonomists of complex groups. Future classifications of groups affected by parallelism are likely to require data from detailed, multi-disciplinary studies of key characters to interpret phylogenies correctly. (C) 2016 Elsevier GmbH. All rights reserved.