Summary :The Apicomplexa is traditionally considered to contain four clearly defined groups, but the phylogenetic relationships among these groups, and their subsequent taxonomic arrangement, are currently unclear. Here, I consider five of the important criteria that need to be met before radical taxonomic changes are made, in relation to phylogenetic analyses. Unfortunately, at least four of these criteria indicate that the prospects for elucidating the phylogeny and taxonomy of the Apicomplexa are not good in the short term. A lot more pertinent data need to be collected, both in terms of taxa sampled and genes sequenced, before any concordance among phylogenies is likely to emerge; and someone (e.g. a consortium) needs to co-ordinate the active collection and analysis of these data if any worthwhile progress is to be made.