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Background  NK genes are a group of homeobox transcription factors that are involved in various molecular pathways across bilaterians. They are typically divided into two subgroups, the NK cluster (NKC) and NK-linked genes (NKL). While the NKC genes have been studied in various bilaterians, corresponding data of many NKL genes are missing to date. To further investigate the ancestral roles of NK family genes, we analyzed the expression patterns of NKL genes in the onychophoran  Euperipatoides rowelli .    Results  The NKL gene complement of  E. rowelli  comprises eight genes, including  BarH ,  Bari ,  Emx ,  Hhex ,  Nedx ,  NK2.1 ,  vax  and  NK2.2 , of which only  NK2.2  was studied previously. Our data for the remaining seven NKL genes revealed expression in different structures associated with the developing nervous system in embryos of  E. rowelli . While  NK2.1  and  vax  are expressed in distinct medial regions of the developing protocerebrum early in development,  BarH ,  Bari ,  Emx ,  Hhex  and  Nedx  are expressed in late developmental stages, after all major structures of the nervous system have been established. Furthermore,  BarH  and  Nedx  are expressed in distinct mesodermal domains in the developing limbs.    Conclusions  Comparison of our expression data to those of other bilaterians revealed similar patterns of  NK2.1 ,  vax ,  BarH  and  Emx  in various aspects of neural development, such as the formation of anterior neurosecretory cells mediated by a conserved molecular mechanism including  NK2.1  and  vax , and the development of the central and peripheral nervous system involving  BarH  and  Emx . A conserved role in neural development has also been reported from  NK2.2 , suggesting that the NKL genes might have been primarily involved in neural development in the last common ancestor of bilaterians or at least nephrozoans (all bilaterians excluding xenacoelomorphs). The lack of comparative data for many of the remaining NKL genes, including  Bari ,  Hhex  and  Nedx  currently hampers further evolutionary conclusions. Hence, future studies should focus on the expression of these genes in other bilaterians, which would provide a basis for comparative studies and might help to better understand the role of NK genes in the diversification of bilaterians.    Electronic supplementary material  The online version of this article (10.1186/s12861-019-0185-9) contains supplementary material, which is available to authorized users.

Expression of NK genes that are not part of the NK cluster in the onychophoran Euperipatoides rowelli (Peripatopsidae)