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The immense diversity in body morphology and life cycle strategies in copepod crustaceans that we witness today can be viewed as the result of hundreds of millions of years of evolution and experimentation with form and function. The tremendous morphological plasticity displayed by symbiotic copepods continues to defy our attempts to confidently place highly divergent body plans in the copepod Tree of Life on morphology alone. It is now widely accepted that the infusion of molecular biology into the study of copepod evolution is a large part of the solution to this problem and that molecular phylogenetics is a particularly promising generator of new insights. Although a robust scheme of interrelationships between the various lineages of fish parasites (particularly within the Siphonostomatoida) has started to emerge in recent years by analyzing molecular sequence data, the picture is far less clear with regard to the phylogenetic position of the plethora of families that utilize invertebrates as hosts, simply because such data have not been available so far for many of the highly modified families. This is particularly applicable to the various morphologically bizarre taxa that are associated with cnidarians, polychaete worms and mollusc hosts, and lack any external evidence in support of their copepod identity. Although no extant taxa are truly intermediate in a direct phylogenetic (ancestor–descendant) sense, the degree to which they can shed light on the stepwise evolution of body plans depends on their position in a tree. Some lineages such as the Fratiidae and Erebonasteridae have been viewed as intermediate taxa or so-called “missing links” based on the presence of a mosaic of morphological character states that allowed for phylogenetic inferences to be made. Testing these scenarios with molecular data has deposed these lineages from their intermediate positions, instead exposing them as evolutionary cul-de-sacs. Despite the recent publication of various molecular-based large-scale phylogenies (some of which became subjected to reanalysis and fierce criticism) which initially inspired hope that we will eventually achieve a fully resolved copepod tree, the selected examples in this presentation demonstrate that copepod phylogenetics has not approached a tipping point yet and that connecting the dots may well be substantially more difficult than drafting the tree in the first place.