An increasing number of paleobiological studies use preexisting cladistic data sets to estimate shifting lev-els of morphological disparity over time, and investigate the relative positions of taxa within a multivariate morphospace. Although these patterns are derived from characters selected to reconstruct phylogenetic relationships, it is sometimes suggested that they also reflect functional or ecological variation. We test this assertion using a purpose-built matrix of functional mandibular traits and 24 published cladistic matrices targeting early jawed vertebrates. We find that distance matrices calculated from functional and cladistic data are significantly correlated, but that substantial variation in functional dissimilarity goes unexplained by variation in cladistic dissimilarity. Agreement sequentially improves, but not drastically, when cladistic characters are limited to those pertaining to the skull and then mandible. When dissimilarity matrices are subjected to principal coordinate analysis to yield multivariate morphospaces, we find no clear relationship between phylogenetically independent contrasts for scores on lower functional and cladistic coordinate axes. However, we do find that a majority of variation on the first axis of ordinations based on cladistic characters can be explained by phylogeny, even though the distance matrices underlying these ordinations are phenetic. A resampling procedure reveals a positive, but weak, correlation between cladistic and functional disparity measures for equivalent sets of taxa. Although our results show nonrandom relationships between disparity patterns extracted from functional and cladistic character sets, we conclude that these relationships are not sufficiently strong to allow clear inferences about functional variation to be drawn from data assembled for phylogenetic reconstruction.