Recently, a new phylogenetic method employing intron position sharing across species was proposed and support for a Coelomate clade reported (Zheng et al. 2007. A rigorous analysis of the pattern of intron conservation supports the Coelomata clade of animals. Mol Biol Evol. 24:2583-2592.). Here, we show that the previous analysis depends on: 1) an idiosyncratic definition of "conserved" introns, 2) exclusion of all phylogenetically informative introns present in outgroups, 3) incorrect inference of change along the critical branch, and 4) lack of variation in rates across branches. The method thus seems unlikely to give accurate results. In addition, we address differences in rates of loss across intron sites, which Zheng et al. claimed invalidates our previous analysis that supported Ecdysozoa (Roy and Gilbert. 2005a. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408.). Instead, we show that our conclusions are likely to be robust to such concerns.