Different views on recognising taxa associated with the Campomanesia xanthocarpa group (Myrtaceae) demonstrate the difficulties in clearly delimiting species. Studies using Inter Simple Sequence Repeats (ISSR) molecular markers were carried out on 201 individuals from 13 populations of C. xanthocarpa Mart. ex O.Berg, C. adamantium (Cambess.) O.Berg, C. costata M.Ibrahim & Landrum and C. littoralis D.Legrand in an attempt to improve understanding of species boundaries between these species. SplitsTree, analysis of molecular variance (AMOVA), principal component analysis (PCA), Neighbour-Joining (NJ) dendrogram and STRUCTURE showed inconsistencies between morphological and genetic data in these taxa. Therefore C. adamantium and C. xanthocarpa are treated as distinct taxa in this study, as are C. costata, C. littoralis and C. rhombea O.Berg that were previously considered part of C. xanthocarpa. Structured populations in C. adamantium were not congruent with taxonomic data or poorly supported in the data analysed. These were maintained as a single polymorphic species and new integrative approaches are necessary to improve understanding of taxon boundaries. We present a taxonomic treatment based on these decisions. This study contributes to the systematic treatment of Campomanesia and encourages specific delimitation studies to resolve remaining taxonomic issues within the genus.