The species diversity of the phylum Rotifera has been largely studied on the 
basis of morphological characters. However, cladistic relationships within this 
group are poorly resolved due to extensive homoplasy in morphological traits, 
substantial phenotypic plasticity and a poor fossil record. We undertook this 
study to determine if a phylogeny based on partial 18S rDNA, which included the 
helix E23 of 18S rDNA sequence, was concordant with established taxonomic 
relationships within the order Ploimida (class: Monogononta). We also estimated 
the level of polymorphism within clones and populations of Ploimida 'species'. 
Finally, we included the Cycliophora Symbion pandora as outgroup and the 
variable helix E23 region to examine the influence of their signal on the 
evolutionary relationships among Acanthocephala, Bdelloidea and Ploimida. 
Phylogenetic reconstruction was performed using maximum parsimony, neighbour 
joining and maximum likelihood methods. We found 1) that morphologically similar 
Ploimida 'species' show vastly different 18S E23 rDNA sequences; 2) inclusion of 
the helix E23 of 18S rDNA and its secondary structure analysis results in better 
resolution of family level relationships within the Ploimida; 3) an impact of 
Symbion pandora as an outgroup with inclusion of the helix E23 on the 
relationships between the Rotifera and the Acanthocephala; and 4) partial 
incongruence and differential substitution rate between conserved region and 
helix E23 region of the 18S rDNA gene depending on the taxomic group studied.