Entonaema, Pulveria, Phylacia, Rhopalostroma, Sarcoxylon and Thamnomyces are relatively small and poorly studied genera of Xylariaceae. Their affinities to the mainstream of the family largely remain to be evaluated. Secondary metabolite profiles of type materials, recently collected specimens, and cultures, were generated to address this problem from a chemotaxonomic point of view. Micro-scale extraction and subsequent analytical HPLC with UV/visual (diode array) and ms detection in the positive and negative Electrospray mode were carried out, employing spectral libraries and standardised gradients that had been optimised to detect characteristic pure compounds in species of allied genera. Surprisingly, the characteristic metabolites had frequently remained stable even in specimens collected up to 190 years ago. Hence, this methodology not only proved valuable to establish the conspecificity of type materials with recent records, but also revealed some interesting correlations: (1) Stromatal pigments of Entonaema cinnabarina, E. globosum and E. liquescens are mitorubrins and other characteristic compounds also prevailing in particular species of Hypoxylon; (2) Rhopalostroma, Phylacia, Pulveria and Thamnomyces contain binapththalenes and other compounds typical of Daldinia and Hypoxylon; (3) Sarcoxylon, as well as E. dengii, E. moluccanum and E. pallida, contained none of these pigments, but characteristic yet unknown lipophilic metabolites were detected in their stromatal extracts; (4) Cultures of E. cinnabarina and Rhopalostroma indicum, obtained for the first time, produced essentially the same secondary metabolites that are also typical of Daldinia, but absent in Biscogniauxia, Hypoxylon and other xylariaceous genera. Hence, chemotaxonomic characters reflected the adaptive radiation of this family. Correlations between the evolution of morphological/anatomical characters are discussed.