Cladistic analyses of the interclass relationships of the phylum Echinodermata have not provided a phylogeny that is separately supported by both larval and adult characters. Similar to the reported incongruence with cladistic analyses, molecular analyses of ribosomal RNA (rRNA) genes have also given ambiguous results, which could be due to a number of factors. The use of short sequences, systematic errors such as long branch attraction, and mis-alignments of the data that are introduced by programs which are unsuitable for non-protein coding genes, have resulted in a controversy as to the true nature of echinoderm relationships. Historically, it is the position of the ophiuroids among the five extant classes of echinoderms that has been the most poorly understood, and the most recently published proposal is that there are three plausible relationships, albeit none of these are sufficiently supported. Re-analysis of 28S and 18S rRNA gene sequence data, with the addition of more phylogenetically informative sites as well as new taxa, the use of an alignment procedure that is based on rRNA secondary structure, and the testing of a myriad of evolutionary models have resulted in some new findings of ancestry. Interestingly, it is the phylogenetic position of the ophiuroids that proves to be among the more solid results from this analysis, while the historically supported sister group relationship between the echinoid and holothuroid classes are not greatly corroborated.