Graf and Cummings (2006), hereafter referred to simply as “G & C”, provided phylogenetic analyses of a three-partition data set in order to (1) examine the higher level evolutionary relationships within the Palaeoheterodonta, (2) estimate the history of character state change, and (3) develop a phylogenetic classification for the group. However, portions of the available COI DNA sequence data, for multiple terminals, were omitted from G & C's phylogenetic analyses, and no attempt was made to explicitly account for the documented saturation in the COI data partition. In order to evaluate the effects of these omissions, we performed Bayesian inference (BI) as well as maximum parsimony (MP) analyses on G & C's combined evidence (CE) matrix that included all of the ingroup COI sequences contained in G & C, plus the omitted outgroup COI sequences. We conclude that G & C's COI DNA sequence omissions, when combined with MP analyses not accounting for COI saturation, negatively affected the topologies of the best trees obtained from phylogenetic analyses of the CE matrix. This conclusion questions the utility of G & C's inferences regarding palaeoheterodont bivalve character evolution as well as the taxonomic classification drawn from its preferred topology. For example, counter to G & C's inferences, our BI and “transformed COI” MP analyses determined that unionoid oyster conchology has evolved multiple times, and all of our phylogenetic analyses indicate that the Etheriidae (sensu G & C) is not monophyletic. However, it should be noted that, to date, no phylogenetic analysis of this data set has robustly estimated all basal nodes within the Unionoida. Therefore, any inferences regarding unionoid bivalve character evolution, diversity and classification drawn from these topologies should be considered weakly supported.