Species of Mycosphaerella and their anamorphs are commonly found on the leaves of Myrtaceae, many of which are defoliated by these pathogens. The taxonomy of these fungi has been based on minute morphological differences, and virtually nothing is known regarding their relatedness to each other. In this study, we present a phylogeny of 30 species of Mycosphaerella or their anamorphs from myrtaceous hosts, based on sequence data from the ITS regions of the ribosomal RNA operon. Fifteen of the species were also analysed for the 5′ end of the large subunit (28S), which produced a phylogeny similar to that obtained for the ITS data set. The Mycosphaerella species included in this analysis are all regarded as representatives of section Plaga, and appear to represent a monophyletic assemblage. Mycosphaerella lateralis was the only species shown to have a wide host range. In general, species clustered together based on their anamorph genera. Species with Colletogloeopsis and Stenella anamorphs always grouped in two respective clusters. However, species with Mycovellosiella, Phaeophleospora, Pseudocercospora and Uwebraunia anamorphs occurred separately, suggesting that they have evolved more than once within Mycosphaerella. Based on the ITS data set, all morphospecies were also shown to be phylogenetic species, although too few isolates were available to address questions relating to intraspecies variation. Nevertheless, ITS sequence data proved sufficient to distinguish morphologically similar taxa that have hitherto only been distinguished based on ascospore germination patterns and anamorph characteristics. Sequence data presented in this study should facilitate the identification of Mycosphaerella species occurring on Myrtaceae in the future.