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Among most substantial problems of the modern phylogenetics is integration of molecular and morphological data. Usually molecular phylogenies show some unexpected close relationship of some groups that have been traditionally placed in completely disparate taxa (like nematodes and insects now firmly within the supraphyletic group Ecdysozoa). Here we present a remarkable “reverse” case when detailed morphological data firstly suggested a challenge for traditional taxonomists groupings and then transcriptomic data have robustly confirmed it. Recently a study based on the detailed morphological SEM-data encompassed 178 species from the 16 ophiuroid families showed that the traditional ophiuroid order Euryalida (basket-stars) is closely related to the family of “normal” brittle-stars Ophiuridae (Martynov, 2010) and different from the majority of the other ophiuroid families; the latter forming what appeared to be a big “supergroup”. Such groupings were never suggested in any previous systems and phylogenies of the class Ophiuroidea (Matsumoto, 1917; Mortensen, 1927; Smith et al., 1995). Four years later a large transcriptomic analysis based on 425 genes from 61 species of the 15 ophiuroid families was published (O’Hara et al. 2014). One of the most remarkable results of this analysis is the robustly supported clade of Euryalida+Ophiuridae and a large superclade with the majority of the other ophiuroid families. Thus, this most recent transcriptomic study has robustly confirmed conclusions of the preceding morphological study. This case is clearly contradicts the still widespread opinion that only molecular data can uncover phylogenetic relationships, but most importantly, also clearly shows that of congruence between morphology and molecules is possible, particularly when morphological and molecular approaches are detailed and based on exhaustive taxon sampling. This work was supported by the project ‘‘National Maps of Biodiversity and Connectivity’’ of the Marine Biodiversity Hub, funded through the National Environmental Research Program and administered through the Australian Government Department of the Environment and by the Russian Science Foundation (grant 14-50-00029, SEM study and depository of specimens).