Fossil lignophyte stems show remarkable diversity including non-sympodial and sympodial forms and a variety of pith and tracheid structures. Most lack scalariform bordered pits on radial walls of secondary xylem tracheids, while these occur in the putative progymnosperm Protopitys and some (but not all) cycads, bennettitaleans, and angiosperms. We describe a new genus of Permian gymnosperms that comprises decorticated stems and branches with a parenchymatous pith that is septate in stems but entire in branches and has scleroid cells that are organised singly or in bands. Vasculature is non-sympodial, comprising endarch primary xylem strands that become mesarch leaf traces that are occluded through ontogeny. Secondary xylem is pycnoxylic with scalariform bordered pits on radial tracheid walls. The eustelic and non-sympodial organisation, the septate pith and the presence of scalariform bordered pits on secondary tracheids represent a unique combination of features not previously seen in lignophyte genera, justifying the erection of Xuanweioxylon scalariforme gen. et sp. nov. X. scalariforme shows similarities to several extinct and extant lignophytes but is placed within the coniferophytes — an informal grouping of conifer-like plants of uncertain affinity that includes probable sister groups to cordaitaleans and conifers. Scalariform bordered pitting in secondary tracheids is unique to Xuanweioxylon within coniferophytes, demonstrating previously unrecognised diversity within the group. Results suggest that coniferophytes include intermediates between cordaitaleans and conifers with other lignophytes including Protopitys, pteridosperms, cycads and Bennettitales.