We assessed the ability of three nuclear protein-encoding genes-elongation factor-1alpha (EF-1alpha), RNA polymerase II (Pol II), and elongation factor-2 (EF-2)-from 59 myriapod and 12 non-myriapod species to resolve phylogenetic relationships among myriapod classes and orders. In a previous study using EF-1alpha and Pol II (2134 nt combined) from 34 myriapod taxa, Regier and Shultz recovered widely accepted classes, orders, and families but failed to resolve interclass and interordinal relationships. The result was attributed to heterogenous rates of cladogenesis (specifically, the inability of the slowly evolving sequences to capture phylogenetic signal during rapid phylogenetic diversification) but the possibility of inadequate taxon sampling or limited sequence information could not be excluded. In the present study, the myriapod taxon sample was increased by 25 taxa (73%) and sequence length per taxon was effectively doubled through addition of EF-2 (4318 nt combined). Parsimony and Bayesian analyses of the expanded data set recovered a monophyletic Myriapoda, all four myriapod classes and all multiply sampled orders, often with high node support. However, except for three diplopod clades (Colobognatha, Helminothomorpha, and a subgroup of Pentazonia), few interordinal relationships and no interclass relationships were well supported. These results are similar to those of the earlier study by Regier and Shultz, which indicates that taxon sample and sequence length alone do not readily explain the weakly supported resolution in the earlier study. We review recent paleontological evidence to further develop our proposal that heterogeneity in phylogenetic signal provided by our slowly evolving sequences is due to heterogeneity in the temporal structure of myriapod diversification.