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Background  The Caligidae is a family of parasitic copepods containing over 30 recognised genera. They are commercially important parasites as they cause disease in numerous finfish aquaculture facilities globally. Morphological features are used to distinguish between the genera and  Pseudocaligus  has traditionally been differentiated from  Caligus  solely by the presence of a much reduced form of the fourth thoracic leg. Currently there are numerous DNA sequences available for  Caligus  spp. but only the type species,  Pseudocaligus brevipedis , has molecular data available, so systematic studies using molecular phylogenetic analyses have been limited.    Methods  Three gene regions, SSU rDNA, 16S and CO1, for  Pseudocaligus fugu  from puffer fish from Japan and  Pseudocaligus uniartus  from rabbit fish from Indonesia are sequenced and molecular phylogenetic analyses performed in order to infer phylogenetic relationships between  Pseudocaligus  and other caligid copepods.    Results  The analysis revealed that there was no discrete grouping of  Pseudocaligus  spp. and that they had a polyphyletic distribution within  Caligus  taxa.  Pseudocaligus fugu  grouped with  Caligus elongatus  and contained a unique synapomorphy in the SSU rDNA region only seen in members of that clade.  Pseudocaligus uniartus  formed a well-supported group, in the SSU rDNA analyses, with a  Caligus  sp. that also infects rabbit fish, but was unresolved in the other analyses.  Pseudocaligus brevipedis  consistently and robustly grouped with  Caligus curtus  and  C. centrodonti  in all analyses. The majority of  Lepeophtheirus  spp. form a monophyletic sister group to the  Caligus  clade; however,  L. natalensis  is unresolved in all analyses and does not form part of the main  Lepeophtheirus  clade.    Conclusions  These findings do not support the morphological-based distinction between  Pseudocaligus  and  Caligus , suggesting that the reduced fourth leg is a feature that has evolved on multiple occasions throughout caligid evolution. Congruent molecular phylogenetic data support groupings based on the presence of morphological features, such as lunules, geography and host fish type rather than appendage morphology. Therefore, we support the synonymy of  Pseudocaligus  with  Caligus .

Multiple gene analyses of caligid copepods indicate that the reduction of a thoracic appendage in Pseudocaligus represents convergent evolution