Species of Diaporthe are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of Citrus spp. are revised. Three species of Diaporthe occurring on Citrus are characterised, including D. citri, D. cytosporella and D. foeniculina. Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-α were used to resolve species on Citrus and related Diaporthe species. Diaporthe citri occurs on Citrus throughout the Citrus-growing regions of the world. Diaporthe cytosporella is found on Citrus in Europe and California (USA). Diaporthe foeniculina, including the synonym D. neotheicola, is recognised as a species with an extensive host range including Citrus. Diaporthe medusaea, a name widely used for D. citri, was determined to be a synonym of D. rudis, a species with a broad host range. Diaporthe citri is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. Diaporthe cytosporella, D. foeniculina and D. rudis are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies. Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.