We describe the first molecular and morphological analysis of extant crinoid highlevel inter-relationships. Nuclear and mitochondrial gene sequences and a cladistically coded matrix of 30 morphological characters are presented, and analysed by phylogenetic methods.The molecular data were compiled from concatenated nuclear-encoded 18S rDNA, internal transcribed spacer 1, 5.8S rDNA, and internal transcribed spacer 2, together with part of mitochondrial 16S rDNA, and comprised 3593 sites, of which 313 were parsimonyinformative. The molecular and morphological analyses include data from the bourgueticrinid, Bathycrinus; the antedonid comatulids, Dorometra and Florometra; the cyrtocrinids Cyathidium, Gymnocrinus, and Holopus; the isocrinids Endoxocrinus, and two species of Metacrinus; as well as from Guillecrinus and Caledonicrinus, whose ordinal relationships are uncertain, together with morphological data from Proisocrinus. Because the molecular data include indel-rich regions, special attention was given to alignment procedure, and it was found that relatively low, gene-specific, gap penalties gave alignments from which congruent phylogenetic information was obtained from both well-aligned, indel-poor and potentially misaligned, indel-rich regions. The different sequence data partitions also gave essentially congruent results. The overall direction of evolution in the gene trees remains uncertain: an asteroid outgroup places the root on the branch adjacent to the slowly-evolving isocrinids (consistent with palaeontological order of first appearances), but maximum likelihood analysis with a molecular clock places it elsewhere. Despite lineage-specific rate differences, the clock Only an unusual, divergent 18S rDNA sequence was obtained from the morphologically strange cyrtocrinid Cyathidium. Although not analysed in detail, features of this sequence suggested that it may be a PCR artefact, so that the apparenly basal position of this taxon requires confirmation. If not an artefact, Cyathidium either diverged from the crinoid stem much earlier than has been reognized hitherto (i.e., it may be a Palaeozoic relic), or it has an atypically high rate of molecular evolution.