The genera Ophiophragmus and Amphiodia are amphiurids that are considered taxonomically difficult due to their great resemblance, few diagnostic characters and synonymy problems. Our aim is to redescribe the species using scanning electron microscopy and morphometry of diagnostic structures, and to provide new information for the identification of these Ophiuroidea. Five Amphiodia spp. and six Ophiophragmus spp. recorded in Brazil were rigorously redescribed. The descriptions include new diagnostic characters derived from external morphology, arm microstructures and morphometry. We also provided comparative analyses of species with shared characters such as Amphiodia riisei and Amphiodia trychna. The geographic and bathymetric distributions of the studied species were updated, and new records are provided. All the information presented may be used in taxonomic, ecological and phylogenetic studies, helping to fill gaps in the knowledge of the biodiversity, ecology and evolution of these Ophiuroidea. Conclusively, all the tools applied here assisted in the identification of genera and species and could be useful in other taxonomic studies of Echinodermata.