A milestone in understanding the order's composition came from Smith, Liew, and Hyde's 2003 molecular phylogenetics study, which established the Xylariales as a monophyletic group containing seven families: Amphisphaeriaceae, Apiosporaceae, Clypeosphaeriaceae, Diatrypaceae, Graphostromataceae, Hyponectriaceae, and Xylariaceae.

Their asci, which contained eight spores, featured a distinctive apical structure that stained blue in iodine (a J+ reaction), and their paraphyses (specialised sterile filaments) were free at the tips and originated from the hymenium.

[2] The early molecular studies of the 2000s, while groundbreaking in establishing the monophyly of the order, also revealed limitations in using ribosomal DNA sequences for resolving family-level relationships within the Xylariales.

The relatively low genetic variation observed in commonly used molecular markers presented challenges for understanding the precise relationships between families, leaving many questions about internal phylogenetic structure unresolved.

This evolutionary timeline aligns with important diversification events, including the development of novel stromatic forms and pigmentation in ascospores, traits that distinguish many Xylariales species.

[6] Ancestral state reconstruction studies indicate that early members of Xylariales likely had inconspicuous, immersed ascomata with hyaline, septate ascospores lacking germ slits.

Surveys of genomes from multiple Xylariales species, including economically important genera such as Xylaria and Daldinia, failed to identify canonical mating-type genes MAT1-1-1 and MAT1-1-2.

Advances in genome sequencing have facilitated the identification of biosynthetic gene clusters, revealing insights into the molecular basis of these metabolites and opening new possibilities for synthetic biology applications.

This integrated approach, which combines chemical, genetic, and ecological data, continues to expand the understanding of the functional biodiversity of Xylariales and their role in natural ecosystems.