Neural crest cells (NCCs) and neuromesodermal progenitors (NMPs) are multipotent cells that are important for development of vertebrate embryos. In embryos of ascidians, which are the closest invertebrate relatives of vertebrates, several cells located at the border between the neural plate and the epidermal region have NCC-like properties; hence, their last common ancestor may have had primitive cells like NCCs. However, these ascidian NCC-like cells do not produce cells that are commonly of mesodermal origin. Here, we showed that a cell population located in the lateral to posterior border of the neural plate has properties resembling those of vertebrate NCCs and NMPs. Among them, cells with Tbx6-related expression contribute to muscle near the tailbud, and cells with Sox1/2/3 expression give rise to the nerve cord. These observations and cross-species transcriptome comparison indicates that these cells have properties like those of NMPs. Meanwhile, transcription factor genes Dlx.b, Zic-r.b, and Snai, which are reminiscent of a gene circuit in vertebrate NCCs, are involved in activation of Tbx6-related.b. Thus, the last common ancestor of ascidians and vertebrates may have had cells with hybrid properties of NMPs and NCCs, and such ancestral cells may have produced cells commonly of ectodermal and mesodermal origins.